Construction of prediction model for fetal growth restriction during first trimester in an Asian population

OBJECTIVE

To construct a prediction model for fetal growth restriction (FGR) during the first trimester of pregnancy and evaluate its screening performance.

METHODS

This was a prospective cohort study of singleton pregnancies that underwent routine ultrasound screening at 11 to 13 + 6 weeks at the Affiliated Suzhou Hospital of Nanjing Medical University between January 2019 and April 2022. Basic clinical information, ultrasound indicators and serum biomarkers of pregnant women were collected. Fetal weight assessment was based on the fetal growth curve for the Southern Chinese population. FGR was diagnosed according to Delphi consensus criteria. Least absolute shrinkage and selection operator (lasso) regression was used to select variables for inclusion in the model. Discrimination, calibration and clinical effectiveness of the model were evaluated in training and validation cohorts.

RESULTS

A total of 1188 pregnant women were included, of whom 108 had FGR. Lasso regression identified seven predictive features, including history of maternal hypertension, maternal smoking or passive smoking, gravidity, uterine artery pulsatility index, ductus venosus pulsatility index and multiples of the median values of placental growth factor and soluble fms-like tyrosine kinase-1. The nomogram prediction model constructed from these seven variables accurately predicted FGR, and the area under the receiver-operating-characteristics curve in the validation cohort was 0.82 (95% CI, 0.74-0.90). The calibration curve and Hosmer-Lemeshow test demonstrated good calibration, and the clinical decision curve and clinical impact curve supported its practical value in a clinical setting.

CONCLUSION

The multi-index prediction model for FGR has good predictive value during the first trimester. © 2023 The Authors. Ultrasound in Obstetrics & Gynecology published by John Wiley & Sons Ltd on behalf of International Society of Ultrasound in Obstetrics and Gynecology.

Divergent Selection in Low Recombination Regions Shapes the Genomic Islands in Two Incipient Shorebird Species

Speciation in the face of gene flow is usually associated with a heterogeneous genomic landscape of divergence in nascent species pairs. However, multiple factors, such as divergent selection and local recombination rate variation, can influence the formation of these genomic islands. Examination of the genomic landscapes of species pairs that are still in the early stages of speciation provides an insight into this conundrum. In this study, population genomic analyses were undertaken using a wide range of sampling and whole-genome resequencing data from 96 unrelated individuals of Kentish plover (Charadrius alexandrinus) and white-faced plover (Charadrius dealbatus). We suggest that the two species exhibit varying levels of population admixture along the Chinese coast and on the Taiwan Island. Genome-wide analyses for introgression indicate that ancient introgression had occurred in Taiwan population, and gene flow is still ongoing in mainland coastal populations. Furthermore, we identified a few genomic regions with significant levels of interspecific differentiation and local recombination suppression, which contain several genes potentially associated with disease resistance, coloration, and regulation of plumage molting and thus may be relevant to the phenotypic and ecological divergence of the two nascent species. Overall, our findings suggest that divergent selection in low recombination regions may be a main force in shaping the genomic islands in two incipient shorebird species.

Fine-mapping of a major locus for Fusarium wilt resistance in flax (Linum usitatissimum L.)

KEY MESSAGE

Fine-mapping of a locus on chromosome 1 of flax identified an S-lectin receptor-like kinase (SRLK) as the most likely candidate for a major Fusarium wilt resistance gene. Fusarium wilt, caused by the soil-borne fungal pathogen Fusarium oxysporum f. sp. lini, is a devastating disease in flax. Genetic resistance can counteract this disease and limit its spread. To map major genes for Fusarium wilt resistance, a recombinant inbred line population of more than 700 individuals derived from a cross between resistant cultivar 'Bison' and susceptible cultivar 'Novelty' was phenotyped in Fusarium wilt nurseries at two sites for two and three years, respectively. The population was genotyped with 4487 single nucleotide polymorphism (SNP) markers. Twenty-four QTLs were identified with IciMapping, 18 quantitative trait nucleotides with 3VmrMLM and 108 linkage disequilibrium blocks with RTM-GWAS. All models identified a major QTL on chromosome 1 that explained 20-48% of the genetic variance for Fusarium wilt resistance. The locus was estimated to span ~ 867 Kb but included a ~ 400 Kb unresolved region. Whole-genome sequencing of 'CDC Bethune', 'Bison' and 'Novelty' produced ~ 450 Kb continuous sequences of the locus. Annotation revealed 110 genes, of which six were considered candidate genes. Fine-mapping with 12 SNPs and 15 Kompetitive allele-specific PCR (KASP) markers narrowed down the interval to ~ 69 Kb, which comprised the candidate genes Lus10025882 and Lus10025891. The latter, a G-type S-lectin receptor-like kinase (SRLK) is the most likely resistance gene because it is the only polymorphic one. In addition, Fusarium wilt resistance genes previously isolated in tomato and Arabidopsis belonged to the SRLK class. The robust KASP markers can be used in marker-assisted breeding to select for this major Fusarium wilt resistance locus.

Chromosome-scale Genome assembly of the critically endangered White-eared Night-Heron (Gorsachius magnificus)

The White-eared Night-Heron (Gorsachius magnificus, G. magnificus) is a critically endangered heron that is very poorly known and only found in southern China and northern Vietnam, with an estimated population of 250 to 999 mature individuals. However, the lack of a reference genome has hindered the implementation of conservation management efforts. In this study, we present the first high-quality chromosome-scale reference genome, which was assembled by integrating PacBio long-reads sequencing, Illumina paired-end sequencing, and Hi-C technology. The genome has a total length of 1.176 Gb, with a scaffold N50 of 84.77 Mb and a contig N50 of 18.46 Mb. Utilizing Hi-C data, we anchored 99.89% of the scaffold sequences onto 29 pairs of chromosomes. Additionally, we identified 18,062 protein-coding genes in the genome, with 95.00% of which were functionally annotated. Notably, BUSCO assessment confirmed the presence of 97.2% of highly conserved Aves genes within the genome. This chromosome-level genome assembly and annotation will be valuable for future investigating the G. magnificus's evolutionary adaptation and conservation.

Beyond Vision: A View from Eye to Alzheimer's Disease and Dementia

With the aging of the global population, the health care burden of Alzheimer's disease (AD) and dementia is considered to increase dramatically in the coming decades. Given the insufficiency of effective interventions for AD and dementia, clinical research on identifying potentially modifiable risk factors and early diagnostic biomarkers becomes a public health priority. Currently, extracerebral manifestations with a large proportion of ocular involvement are usually recognized to precede the symptoms of AD and dementia. Growing epidemiologic evidence also suggests that eye disorders, such as cataracts, age-related macular degeneration, glaucoma, diabetic retinopathy, and so on, are closely associated with and even have a higher incidence of AD and dementia. The eye, as an extension of the central nervous system, therefore has the potential to provide a feasible approach to detecting structural and functional abnormalities of the brain. Numerous new imaging modalities are developed and give novel insights into the detection of several neurodegenerative, vascular, neuropathological, and other ocular abnormalities of AD and dementia in scientific research and clinical application. This review provides an overview of the epidemiologic associations between eye disorders and AD or dementia and summarizes the recent advances in ocular examinations and techniques employed for the detection of AD and dementia. With more brain-and-eye interconnections being identified, the eye is becoming a noninvasive and easily accessible window for the early diagnosis and prevention of AD and dementia.

Dose-related effects of early-life intake of sn-2 palmitate, a specific positionally distributed human milk fatty acid, on the composition and metabolism of the intestinal microbiota

sn2 Palmitate in human milk plays an important role in the physiological health of infants by reducing mineral loss, improving stool hardness, and relieving constipation. Also, sn-2 palmitate modulates intestinal microbiota. However, it remains unclear whether the effects of sn-2 palmitate on infant gut microbiota are dose-dependent. In this study, we investigated the effects of low, medium, and high doses (600, 1,800, and 5,400 mg/kg body weight, respectively) of sn-2 palmitate on the structure, composition, and metabolic function of intestinal microbes in mice. Our results showed that high doses of sn-2 palmitate significantly modulated α- and β-diversity of the intestinal microbiota. The relative abundance of Lachnospiraceae_NK4A136_group decreased with increasing doses of sn-2 palmitate. In contrast, the abundances of Bacteroidetes phylum, Bacteroides, uncultured_Lachnospiraceae, and uncultured_Muribaculaceae were positively correlated with sn-2 palmitate doses. The number of genes predicted encoding autophagy-yeast, phospholipase D signaling pathway, and pentose and glucuronate interconversion metabolic functions of intestinal microbiota increased with increasing doses of sn-2 palmitate. In addition, low and medium doses of sn-2 palmitate significantly upregulated the arginine and proline metabolic pathways, and high doses of sn-2 palmitate significantly increased purine metabolism. Our results revealed that the effects of sn-2 palmitate intake early in life on the composition and metabolism of the intestinal microbiota of mice showed dose-related differences. The study is expected to provide a scientific basis for the development of infant formulas.

Risk factors for portal vein system thrombosis after partial splenic embolisation in cirrhotic patients with hypersplenism

AIM

To determine risk factors for portal venous system thrombosis (PVST) after partial splenic artery embolisation (PSAE) in cirrhotic patients with hypersplenism.

MATERIALS AND METHODS

Between March 2014 and February 2022, 428 cirrhotic patients with hypersplenism underwent partial splenic artery embolisation and from these patients 208 were enrolled and 220 were excluded. Medical records of enrolled patients were collected. Computed tomography (CT) images were reviewed by two blinded, independent radiologists. Statistical analyses were performed by using SPSS.

RESULTS

Progressive PVST was observed in 18.75% (39/208) of cirrhotic patients after PSAE. No significant differences in peripheral blood counts, liver function biomarkers, and renal function were observed between the patients with progressive PVST and the patients without progressive PVST. The imaging data showed significant differences in PVST, the diameters of the portal, splenic, and superior mesenteric veins between the progressive PVST group and non-progressive PVST group. Univariate and multivariate analysis demonstrated portal vein thrombosis, spleen infarction percentage, and the diameter of the splenic vein were independent risk factors for progressive PVST. Seventeen of 173 (9.83%) patients showed new PVST; the growth of PVST was observed in 62.86% (22/35) of the patients with pre-existing PVST. Spleen infarction percentage and the diameter of the splenic vein were independent risk factors for new PVST after PSAE.

CONCLUSION

The present study demonstrated portal vein thrombosis, spleen infarction percentage, and the diameter of the splenic vein were independent risk factors for PVST after PSAE in cirrhotic patients with hypersplenism.

[Orodental phenotype and genotype findings in 8 Chinese children with hypophosphatasia]

Objective: To analyze the oral phenotype and gene variation of children with hypophosphatasia (HPP), and explore the genotype-phenotype correlations. Methods: Eight children diagnosed with HPP from January 2008 to January 2023 in Children's Hospital,Zhejiang University School of Medicine were recruited in this study. The pathogenic genes of 5 of them were sequentially analyzed and all of their oral manifestations, laboratory tests and genetic variation types were retrospectively analyzed. Results: A total of 8 children were recruited in the study, 3 males and 5 females, aged from 20 months to 104 months, whose main complaints were premature deciduous tooth loss. Among them, 3 children were diagnosed with odonto HPP, and the other 5 children were diagnosed with childhood HPP, including 2 children was odonto HPP at the first diagnosis and modified as childhood HPP at the age of 5. The age range of first deciduous tooth loss is 9 to 18 months, and the age range of diagnosis is 20 to 104 months. The patients of odonto HPP only showed premature loss of deciduous anterior tooth, while the patients with childhood HPP also showed premature loss of multiple deciduous molars. Panoramic radiographic film revealed enlarged pulp chambers and radicular canals in some primary and permanent teeth. The enamel hypoplasia, hypoplastic short roots, and alveolar resorption of deciduous molar were observed in some cases. The serum alkaline phosphatase (ALP) (30-107 U/L) levels of all the patients were lower than that in the normal children of same age and gender, and the ALP value of the 1-3 years old girls with childhood HPP (30-33 U/L) was lower than that of the three children with odonto HPP (61-107 U/L), but there was no significant difference in statistical analysis. There were 8 variation sites of ALP liver/bone/kidney (ALPL) gene detected in 5 children and their families, all of which were missense variation, including the new variants in the mutations of c.1334C>G(p.Ser445Cys) and c.1259G>T(p.Gly420Val) that were not reported in the literature. One case was autosomal dominant inheritance and other 4 cases were complex heterozygous variation with autosomal recessive inheritance. Conclusions: Pediatric stomatologists are often the first doctors to detect childhood and odonto HPP. Diagnosis of mild HPP is often delayed. The severity of HPP is related to serum ALP level and ALPL gene mutation sites.

Temporal Structures in Positron Spectra and Charge-Sign Effects in Galactic Cosmic Rays

We present the precision measurements of 11 years of daily cosmic positron fluxes in the rigidity range from 1.00 to 41.9 GV based on 3.4×10^{6} positrons collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The positron fluxes show distinctly different time variations from the electron fluxes at short and long timescales. A hysteresis between the electron fluxes and the positron fluxes is observed with a significance greater than 5σ at rigidities below 8.5 GV. On the contrary, the positron fluxes and the proton fluxes show similar time variation. Remarkably, we found that positron fluxes are modulated more than proton fluxes with a significance greater than 5σ for rigidities below 7 GV. These continuous daily positron fluxes, together with AMS daily electron, proton, and helium fluxes over an 11-year solar cycle, provide unique input to the understanding of both the charge-sign and mass dependencies of cosmic rays in the heliosphere.

Hidden Genetic Regulation of Human Complex Traits via Brain Isoforms

Alternative splicing exists in most multi-exonic genes, and exploring these complex alternative splicing events and their resultant isoform expressions is essential. However, it has become conventional that RNA sequencing results have often been summarized into gene-level expression counts mainly due to the multiple ambiguous mapping of reads at highly similar regions. Transcript-level quantification and interpretation are often overlooked, and biological interpretations are often deduced based on combined transcript information at the gene level. Here, for the most variable tissue of alternative splicing, the brain, we estimate isoform expressions in 1,191 samples collected by the Genotype-Tissue Expression (GTEx) Consortium using a powerful method that we previously developed. We perform genome-wide association scans on the isoform ratios per gene and identify isoform-ratio quantitative trait loci (irQTL), which could not be detected by studying gene-level expressions alone. By analyzing the genetic architecture of the irQTL, we show that isoform ratios regulate educational attainment via multiple tissues including the frontal cortex (BA9), cortex, cervical spinal cord, and hippocampus. These tissues are also associated with different neuro-related traits, including Alzheimer's or dementia, mood swings, sleep duration, alcohol intake, intelligence, anxiety or depression, etc. Mendelian randomization (MR) analysis revealed 1,139 pairs of isoforms and neuro-related traits with plausible causal relationships, showing much stronger causal effects than on general diseases measured in the UK Biobank (UKB). Our results highlight essential transcript-level biomarkers in the human brain for neuro-related complex traits and diseases, which could be missed by merely investigating overall gene expressions.

Supplementary Information

The online version contains supplementary material available at 10.1007/s43657-023-00100-6.

Properties of Cosmic-Ray Sulfur and Determination of the Composition of Primary Cosmic-Ray Carbon, Neon, Magnesium, and Sulfur: Ten-Year Results from the Alpha Magnetic Spectrometer

We report the properties of primary cosmic-ray sulfur (S) in the rigidity range 2.15 GV to 3.0 TV based on 0.38×10^{6} sulfur nuclei collected by the Alpha Magnetic Spectrometer experiment (AMS). We observed that above 90 GV the rigidity dependence of the S flux is identical to the rigidity dependence of Ne-Mg-Si fluxes, which is different from the rigidity dependence of the He-C-O-Fe fluxes. We found that, similar to N, Na, and Al cosmic rays, over the entire rigidity range, the traditional primary cosmic rays S, Ne, Mg, and C all have sizeable secondary components, and the S, Ne, and Mg fluxes are well described by the weighted sum of the primary silicon flux and the secondary fluorine flux, and the C flux is well described by the weighted sum of the primary oxygen flux and the secondary boron flux. The primary and secondary contributions of the traditional primary cosmic-ray fluxes of C, Ne, Mg, and S (even Z elements) are distinctly different from the primary and secondary contributions of the N, Na, and Al (odd Z elements) fluxes. The abundance ratio at the source for S/Si is 0.167±0.006, for Ne/Si is 0.833±0.025, for Mg/Si is 0.994±0.029, and for C/O is 0.836±0.025. These values are determined independent of cosmic-ray propagation.

Temporal Structures in Electron Spectra and Charge Sign Effects in Galactic Cosmic Rays

We present the precision measurements of 11 years of daily cosmic electron fluxes in the rigidity interval from 1.00 to 41.9 GV based on 2.0×10^{8} electrons collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The electron fluxes exhibit variations on multiple timescales. Recurrent electron flux variations with periods of 27 days, 13.5 days, and 9 days are observed. We find that the electron fluxes show distinctly different time variations from the proton fluxes. Remarkably, a hysteresis between the electron flux and the proton flux is observed with a significance of greater than 6σ at rigidities below 8.5 GV. Furthermore, significant structures in the electron-proton hysteresis are observed corresponding to sharp structures in both fluxes. This continuous daily electron data provide unique input to the understanding of the charge sign dependence of cosmic rays over an 11-year solar cycle.

[Association of extranodal extension and lymph node ratio with radioactive iodine-refractory papillary thyroid cancer]

Objective: To investigate the related factors of radioiodine-refractory thyroid cancer (RAIR-DTC) and the increase of cumulative iodine treatment dose. Methods: The data of patients with papillary thyroid cancer who underwent surgery and iodine treatment for the first time in the Affiliated Cancer Hospital of Zhengzhou University from January 2015 to December 2017 were retrospectively analyzed. The related factors of RAIR-DTC and the increase of cumulative iodine treatment dose were explored. Results: A total of 650 patients were enrolled, including 217 males (33.4%) and 433 females (66.6%), aged 45 (34, 53) years. There were 123 patients (18.9%) over 55 years old, 171 patients (26.3%) with extranodal extension and 18 patients (2.8%) with distant metastasis. The median lymph node ratio was 0.22 (0.11, 0.33). Twenty patients (3.1%) had an accumulated iodine treatment dose>400 mCi and 19 patients (2.9%) had RAIR-DTC. Multivariate logistic regression analysis showed that extranodal extension (OR=19.833, 95%CI: 6.057-73.325, P<0.001) was related factors for the increase of cumulative iodine treatment dose. Age>55 years old (OR=3.322, 95%CI: 1.136-9.466, P=0.024), distant metastasis (OR=10.059, 95%CI: 2.508-38.888, P<0.001), extranodal extension (OR=5.278, 95%CI: 1.707-19.813, P=0.006) and lymph node ratio (OR=34.724, 95%CI: 2.749-384.575, P=0.004) were related factors for RAIR-DTC. Conclusions: Extranodal extension and lymph node ratio are related factors for RAIR-DTC. In clinical practice, more attention should be paid to the influence of different lymph node metastasis characteristics on the occurrence of RAIR-DTC and the cumulative therapeutic dose of iodine.

Integrative analysis of multiomics data identifies selenium-related gene ALAD associating with keshan disease

Keshan disease is an endemic fatal dilated cardiomyopathy that can cause heart enlargement, heart failure, and cardiogenic death. Selenium deficiency is considered to be the main cause of Keshan disease. However, the molecular mechanism underlying Keshan disease remains unclear. Our whole-exome sequencing from 68 patients with Keshan disease and 100 controls found 199 candidate genes by gene-level burden tests. Interestingly, using multiomics data, the selenium-related gene ALAD (δ-aminolevulinic acid dehydratase) was the only candidate causative gene identified by three different analysis approaches. Based on single-cell transcriptome data, ALAD was highly expressed in cardiomyocytes and double mutations of human ALAD dramatically reduced its enzyme activity in vitro compared to negative control. Functional analysis of ALAD inhibition in mice resulted in a Keshan phenotype with left ventricular enlargement and cardiac dysfunction, whereas administration of sodium selenite markedly reversed the changes caused by ALAD inhibition. In addition, sodium selenite reversed Keshan phenotypes by affecting energy metabolism and mitochondrial function in mice as shown by the transcriptomic and proteomic data and the ultrastructure of cardiac myocytes. Our findings are the first to demonstrate that the selenium-related gene ALAD is essential for cardiac function by maintaining normal mitochondrial activity, providing strong molecular evidence supporting the hypothesis of selenium deficiency in Keshan disease. These results identified ALAD as a novel target for therapeutic intervention in Keshan disease and Keshan disease-related dilated cardiomyopathy.

Identification and functional characterization of BICD2 as a candidate disease gene in an consanguineous family with dilated cardiomyopathy

Background

Familial dilated cardiomyopathy (DCM) is a genetic cardiomyopathy that is associated with reduced left ventricle function or systolic function. Fifty-one DCM-causative genes have been reported, most of which are inherited in an autosomal dominant manner. However, recessive DCM-causative gene is rarely observed.

Methods

Whole-exome sequencing (WES) was performed in a consanguineous family with DCM to identify candidate variants. Sanger sequencing was utilized to confirm the variant. We then checked the DCM candidate gene in 210 sporadic DCM cases. We next explored BICD2 function in both embryonic and adult bicd2-knockout zebrafish models. In vivo cardiac function of bicd2-knockout fish was detected by echocardiography and RNA-seq.

Results

We identified an autosomal recessive and evolutionarily conserved missense variant, NM_001003800.1:c.2429G > A, in BICD2, which segregated with the disease phenotype in a consanguineous family with DCM. Furthermore, we confirmed the presence of BICD2 variants in 3 sporadic cases. Knockout of bicd2 resulted in partial embryonic lethality in homozygotes, suggesting a vital role for bicd2 in embryogenesis. Heart dilation and decreased ejection fraction, cardiac output and stroke volume were observed in bicd2-knockout zebrafish, suggesting a phenotype similar to human DCM. Furthermore, RNA-seq confirmed a larger transcriptome shift in in bicd2 homozygotes than in heterozygotes. Gene set enrichment analysis of bicd2-deficient fish showed the enrichment of altered gene expression in cardiac pathways and mitochondrial energy metabolism.

Conclusions

Our study first shows that BICD2 is a novel candidate gene associated with familial DCM, and our findings will facilitate further insights into the molecular pathological mechanisms of DCM.

Supplementary Information

The online version contains supplementary material available at 10.1186/s12920-022-01349-y.

Integrative Analyses Identify Potential Key Genes and Calcium-Signaling Pathway in Familial Atrioventricular Nodal Reentrant Tachycardia Using Whole-Exome Sequencing

Background

Atrioventricular nodal reentrant tachycardia (AVNRT) is a common arrhythmia. Growing evidence suggests that family aggregation and genetic factors are involved in AVNRT. However, in families with a history of AVNRT, disease-causing genes have not been reported.

Objective

To investigate the genetic contribution of familial AVNRT using a whole-exome sequencing (WES) approach.

Methods

Blood samples were collected from 20 patients from nine families with a history of AVNRT and 100 control participants, and we systematically analyzed mutation profiles using WES. Gene-based burden analysis, integration of previous sporadic AVNRT data, pedigree-based co-segregation, protein-protein interaction network analysis, single-cell RNA sequencing, and confirmation of animal phenotype were performed.

Results

Among 95 related reference genes, seven candidate pathogenic genes have been identified both in sporadic and familial AVNRT, including CASQ2, AGXT, ANK2, SYNE2, ZFHX3, GJD3, and SCN4A. Among the 37 reference genes from sporadic AVNRT, five candidate pathogenic genes were identified in patients with both familial and sporadic AVNRT: LAMC1, ryanodine receptor 2 (RYR2), COL4A3, NOS1, and ATP2C2. To identify the common pathogenic mechanisms in all AVNRT cases, five pathogenic genes were identified in patients with both familial and sporadic AVNRT: LAMC1, RYR2, COL4A3, NOS1, and ATP2C2. Considering the unique internal candidate pathogenic gene within pedigrees, three genes, TRDN, CASQ2, and WNK1, were likely to be the pathogenic genes in familial AVNRT. Notably, the core calcium-signaling pathway may be closely associated with the occurrence of AVNRT, including CASQ2, RYR2, TRDN, NOS1, ANK2, and ATP2C2.

Conclusion

Our pedigree-based studies demonstrate that RYR2 and related calcium signaling pathway play a critical role in the pathogenesis of familial AVNRT using the WES approach.

[Development and validation of a prognostic model based on SEER data for patients with esophageal carcinoma after esophagectomy]

OBJECTIVE

To develop a nomogram to predict the long-term survival of patients with esophageal cancer following esophagectomy.

METHODS

We collected the data of 7215 patients with esophageal carcinoma from the Surveillance, Epidemiology, and End Results (SEER) database during the period from 2004 and 2016. Of these patients, 5052 were allocated to the training cohort and the remaining 2163 patients to the internal validation cohort using bootstrap resampling, with another 435 patients treated in the Department of Cardiothoracic Surgery of Jinling Hospital between 2014 and 2016 serving as the external validation cohort.

RESULTS

In the overall cohort, the 1-, 3-, and 5-year cancer-specific mortality rates were 14.6%, 35.7% and 41.6%, respectively. Age (≥80 years vs < 50 years, P < 0.001), gender (male vs female, P < 0.001), tumor site (lower vs middle segment, P=0.013), histology (EAC vs ESCC, P=0.012), tumor grade (poorly vs well differentiated, P < 0.001), TNM stage (Ⅳ vs Ⅰ, P < 0.001), tumor size (> 50 mm vs 0-20 mm, P < 0.001), chemotherapy (yes vs no, P < 0.001), and LNR (> 0.25 vs 0, P < 0.001) were identified as independent risk factors affecting long-term survival of the patients. The nomograms established based on the model for predicting the survival probability of the patients at 1, 3 and 5 years after operation showed a C-index of 0.726 (95% CI: 0.714-0.738) for predicting the overall survival (OS) and of 0.735 (95% CI: 0.727-0.743) for cancer-specific survival (CSS) in the training cohort. In the internal validation cohort, the C-index of the nomograms was 0.752 (95% CI: 0.738-0.76) for OS and 0.804 (95% CI: 0.790-0.817) for CSS, as compared with 0.749 (95% CI: 0.736-0.767) and 0.788 (95%CI: 0.751-0.808), respectively, in the external validation cohort. The nomograms also showed a higher sensitivity than the TNM staging system for predicting long-term prognosis.

CONCLUSION

This prognostic model has a high prediction efficiency and can help to identify the high-risk patients with esophageal carcinoma after surgery and serve as a supplement for the current TNM staging system.

Properties of Daily Helium Fluxes

We present the precision measurement of 2824 daily helium fluxes in cosmic rays from May 20, 2011 to October 29, 2019 in the rigidity interval from 1.71 to 100 GV based on 7.6×10^{8} helium nuclei collected with the Alpha Magnetic Spectrometer (AMS) aboard the International Space Station. The helium flux and the helium to proton flux ratio exhibit variations on multiple timescales. In nearly all the time intervals from 2014 to 2018, we observed recurrent helium flux variations with a period of 27 days. Shorter periods of 9 days and 13.5 days are observed in 2016. The strength of all three periodicities changes with time and rigidity. In the entire time period, we found that below ∼7  GV the helium flux exhibits larger time variations than the proton flux, and above ∼7  GV the helium to proton flux ratio is time independent. Remarkably, below 2.4 GV a hysteresis between the helium to proton flux ratio and the helium flux was observed at greater than the 7σ level. This shows that at low rigidity the modulation of the helium to proton flux ratio is different before and after the solar maximum in 2014.

Genetic Landscape of the ACE2 Coronavirus Receptor

BACKGROUND

SARS-CoV-2, the causal agent of COVID-19, enters human cells using the ACE2 (angiotensin-converting enzyme 2) protein as a receptor. ACE2 is thus key to the infection and treatment of the coronavirus. ACE2 is highly expressed in the heart and respiratory and gastrointestinal tracts, playing important regulatory roles in the cardiovascular and other biological systems. However, the genetic basis of the ACE2 protein levels is not well understood.

METHODS

We have conducted the largest genome-wide association meta-analysis of plasma ACE2 levels in >28 000 individuals of the SCALLOP Consortium (Systematic and Combined Analysis of Olink Proteins). We summarize the cross-sectional epidemiological correlates of circulating ACE2. Using the summary statistics-based high-definition likelihood method, we estimate relevant genetic correlations with cardiometabolic phenotypes, COVID-19, and other human complex traits and diseases. We perform causal inference of soluble ACE2 on vascular disease outcomes and COVID-19 severity using mendelian randomization. We also perform in silico functional analysis by integrating with other types of omics data.

RESULTS

We identified 10 loci, including 8 novel, capturing 30% of the heritability of the protein. We detected that plasma ACE2 was genetically correlated with vascular diseases, severe COVID-19, and a wide range of human complex diseases and medications. An X-chromosome cis-protein quantitative trait loci-based mendelian randomization analysis suggested a causal effect of elevated ACE2 levels on COVID-19 severity (odds ratio, 1.63 [95% CI, 1.10-2.42]; P=0.01), hospitalization (odds ratio, 1.52 [95% CI, 1.05-2.21]; P=0.03), and infection (odds ratio, 1.60 [95% CI, 1.08-2.37]; P=0.02). Tissue- and cell type-specific transcriptomic and epigenomic analysis revealed that the ACE2 regulatory variants were enriched for DNA methylation sites in blood immune cells.

CONCLUSIONS

Human plasma ACE2 shares a genetic basis with cardiovascular disease, COVID-19, and other related diseases. The genetic architecture of the ACE2 protein is mapped, providing a useful resource for further biological and clinical studies on this coronavirus receptor.

RNAseq reveals extensive metabolic disruptions in the sensitive SF-295 cell line treated with schweinfurthins

The schweinfurthin family of natural compounds exhibit a unique and potent differential cytotoxicity against a number of cancer cell lines and may reduce tumor growth in vivo. In some cell lines, such as SF-295 glioma cells, schweinfurthins elicit cytotoxicity at nanomolar concentrations. However, other cell lines, like A549 lung cancer cells, are resistant to schweinfurthin treatment up to micromolar concentrations. At this time, the precise mechanism of action and target for these compounds is unknown. Here, we employ RNA sequencing of cells treated with 50 nM schweinfurthin analog TTI-3066 for 6 and 24 h to elucidate potential mechanisms and pathways which may contribute to schweinfurthin sensitivity and resistance. The data was analyzed via an interaction model to observe differential behaviors between sensitive SF-295 and resistant A549 cell lines. We show that metabolic and stress-response pathways were differentially regulated in the sensitive SF-295 cell line as compared with the resistant A549 cell line. In contrast, A549 cell had significant alterations in response genes involved in translation and protein metabolism. Overall, there was a significant interaction effect for translational proteins, RNA metabolism, protein metabolism, and metabolic genes. Members of the Hedgehog pathway were differentially regulated in the resistant A549 cell line at both early and late time points, suggesting a potential mechanism of resistance. Indeed, when cotreated with the Smoothened inhibitor cyclopamine, A549 cells became more sensitive to schweinfurthin treatment. This study therefore identifies a key interplay with the Hedgehog pathway that modulates sensitivity to the schweinfurthin class of compounds.

Periodicities in the Daily Proton Fluxes from 2011 to 2019 Measured by the Alpha Magnetic Spectrometer on the International Space Station from 1 to 100 GV

We present the precision measurement of the daily proton fluxes in cosmic rays from May 20, 2011 to October 29, 2019 (a total of 2824 days or 114 Bartels rotations) in the rigidity interval from 1 to 100 GV based on 5.5×10^{9} protons collected with the Alpha Magnetic Spectrometer aboard the International Space Station. The proton fluxes exhibit variations on multiple timescales. From 2014 to 2018, we observed recurrent flux variations with a period of 27 days. Shorter periods of 9 days and 13.5 days are observed in 2016. The strength of all three periodicities changes with time and rigidity. The rigidity dependence of the 27-day periodicity is different from the rigidity dependences of 9-day and 13.5-day periods. Unexpectedly, the strength of 9-day and 13.5-day periodicities increases with increasing rigidities up to ∼10  GV and ∼20  GV, respectively. Then the strength of the periodicities decreases with increasing rigidity up to 100 GV.

Erratum: Properties of a New Group of Cosmic Nuclei: Results from the Alpha Magnetic Spectrometer on Sodium, Aluminum, and Nitrogen [Phys. Rev. Lett. 127, 021101 (2021)]

This corrects the article DOI: 10.1103/PhysRevLett.127.021101.

Properties of a New Group of Cosmic Nuclei: Results from the Alpha Magnetic Spectrometer on Sodium, Aluminum, and Nitrogen

We report the properties of sodium (Na) and aluminum (Al) cosmic rays in the rigidity range 2.15 GV to 3.0 TV based on 0.46 million sodium and 0.51 million aluminum nuclei collected by the Alpha Magnetic Spectrometer experiment on the International Space Station. We found that Na and Al, together with nitrogen (N), belong to a distinct cosmic ray group. In this group, we observe that, similar to the N flux, both the Na flux and Al flux are well described by the sums of a primary cosmic ray component (proportional to the silicon flux) and a secondary cosmic ray component (proportional to the fluorine flux). The fraction of the primary component increases with rigidity for the N, Na, and Al fluxes and becomes dominant at the highest rigidities. The Na/Si and Al/Si abundance ratios at the source, 0.036±0.003 for Na/Si and 0.103±0.004 for Al/Si, are determined independent of cosmic ray propagation.

[Orexin-A inhibits γ-aminobutyric acid current of neonatal rat spinal cord ventral horn neurons by activating OX1R, OX2R and Ca2+-independent PKC]

OBJECTIVE

To investigate the effect of orexin-A on the functionality of ionotropic γ-aminobutyric acid (GABA) receptors in spinal cord ventral horn neurons and its mechanisms.

OBJECTIVE

The spinal cord containing the lumbosacral enlargement was isolated from neonatal SD rats (7-12 days old) and sliced. The slices were digested with papain (in 0.18 g/30 mL artificial cerebrospinal fluid) for 40-60 min, and the ventral horn neurons were separated acutely using fire-polished Pasteur pipettes. After the cells adhered to the bottom of Petri dishes, patch-clamp experiments combined with pharmacological methods were performed to test the effects of orexin-A on GABA currents of the neurons treated with SB334867 (a selective OX₁R antagonist), TCSOX229 (a selective OX₂R antagonist), Bis-Ⅳ (a PKC inhibitor), PMA (a PKC agonist), Rp-cAMP (a PKA inhibitor), or BAPTA (Ca²⁺ chelator).

OBJECTIVE

The isolated neurons maintained good morphologies with diverse shapes of cell body and long protrusions. Treatment with orexin-A significantly inhibited the amplitude of GABA-induced current (P < 0.001, n=49) with an inhibition rate of (67.48±12.50)%. SB334867 and TCSOX229, when applied simultaneously, completely abolished the suppressive effect of orexin-A on the GABA currents (P=0.93, n=6), and their separate use partially relieved the suppressive effect of orexin-A (P=0.001, n=8; P=0.02, n=8). The application of Bis-Ⅳ also abolished the suppressive effect of orexin-A on GABA currents (P=0.31, n=5). PMA mimicked the effect of orexin-A in these neurons and significantly inhibited GABA currents with an inhibition rate of (60.79±10.94)%, and the application of orexin-A did not cause further suppression of GABA currents in PMA-treated neurons (P=0.15, n=6). Orexin-A was still capable of suppressing GABA currents in Rp-cAMP-treated neurons (P=0.001, n=5). The extracellular Ca²⁺-free solution (P=0.004, n=8) or the presence of BAPTA (P=0.04, n=7) did not significantly affect the inhibitory effect of orexin-A on GABA currents.

OBJECTIVE

Orexin-A inhibits GABA currents in the ventral horn neurons of rat spinal cord probably by activating OX₁R, OX₂R and Ca²⁺-independent PKC.

POS0851 IDENTIFICATION OF HUB GENES AND PATHWAYS IN DERMATOMYOSITIS BY BIOINFORMATICS ANALYSIS

Background:

Dermatomyositis (DM) is a chronic systemic autoimmune disease characterized by inflammatory infiltrates in the skin and muscle1. The genes and pathways in the inflamed myopathies in patients with DM are poorly understood2.

Objectives:

To identify the key genes and pathways associated with DM and further discover its pathogenesis.

Methods:

Muscle tissue gene expression profile (GSE143323) were acquired from the GEO database, which included 39 DM samples and 20 normal samples. The differentially expressed genes (DEGs) in DM muscle tissue were screened by adopting the R software. Gene ontology (GO) and Kyoto Encyclopedia of Genome (KEGG) pathway enrichment analysis was performed by Metascape online analysis tool. A protein-protein interaction (PPI) network was then constructed by STRING software using the genes in significantly different pathways. Network of DEGs was analyzed by Cytoscape software. And degree of nodes was used to screen key genes.

Results:

Totally, 126 DEGs were obtained, which contained 122 up-regulated and 4 down-regulated. GO analysis revealed that most of the DEGs were significantly enriched in type I interferon signaling pathway, response to interferon-gamma, collagen-containing extracellular matrix, response to interferon-alpha and bacterium, positive regulation of cell death, leukocyte chemotaxis. KEGG pathway analysis showed that upregulated DEGs enhanced pathways associated with the hepatitis C, complement and coagulation cascades, p53 signaling pathway, RIG-I-like receptor signaling, Osteoclast differentiation, and AGE-RAGE signaling pathway. Ten hub genes were identified in DM, they were ISG15, IRF7, STAT1, MX1, OASL, OAS2, OAS1, OAS3, GBP1, and IRF9 according to the Cytoscape software and cytoHubba plugin.

Conclusion:

The findings from this bioinformatics network analysis study identified the key hub genes that might provide new molecular markers for its diagnosis and treatment.

References:

[1]Olazagasti JM, Niewold TB, Reed AM. Immunological biomarkers in dermatomyositis. Curr Rheumatol Rep 2015;17(11):68. doi: 10.1007/s11926-015-0543-y [published Online First: 2015/09/26].

[2]Chen LY, Cui ZL, Hua FC, et al. Bioinformatics analysis of gene expression profiles of dermatomyositis. Mol Med Rep 2016;14(4):3785-90. doi: 10.3892/mmr.2016.5703 [published Online First: 2016/09/08].

[3]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

POS0458 IDENTIFICATION OF HUB GENES AND MOLECULAR PATHWAYS IN PATIENTS WITH RHEUMATOID ARTHRITIS BY BIOINFORMATICS ANALYSIS

Background:

Rheumatoid arthritis (RA) is a chronic, inflammatory synovitis based systemic disease of unknown etiology1. The genes and pathways in the inflamed synovium of RA patients are poorly understood.

Objectives:

This study aims to identify differentially expressed genes (DEGs) associated with the progression of synovitis in RA using bioinformatics analysis and explore its pathogenesis2.

Methods:

RA expression profile microarray data GSE89408 were acquired from the public gene chip database (GEO), including 152 synovial tissue samples from RA and 28 healthy synovial tissue samples. The DEGs of RA synovial tissues were screened by adopting the R software. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis were performed. Protein-protein interaction (PPI) networks were assembled with Cytoscape software.

Results:

A total of 654 DEGs (268 up-regulated genes and 386 down-regulated genes) were obtained by the differential analysis. The GO enrichment results showed that the up-regulated genes were significantly enriched in the biological processes of myeloid leukocyte activation, cellular response to interferon-gamma and immune response-regulating signaling pathway, and the down-regulated genes were significantly enriched in the biological processes of extracellular matrix, retinoid metabolic process and regulation of lipid metabolic process. The KEGG annotation showed the up-regulated genes mainly participated in the staphylococcus aureus infection, chemokine signaling pathway, lysosome signaling pathway and the down-regulated genes mainly participated in the PPAR signaling pathway, AMPK signaling pathway, ECM-receptor interaction and so on. The 9 hub genes (PTPRC, TLR2, tyrobp, CTSS, CCL2, CCR5, B2M, fcgr1a and PPBP) were obtained based on the String database model by using the Cytoscape software and cytoHubba plugin3.

Conclusion:

The findings identified the molecular mechanisms and the key hub genes of pathogenesis and progression of RA.

References:

[1]Xiong Y, Mi BB, Liu MF, et al. Bioinformatics Analysis and Identification of Genes and Molecular Pathways Involved in Synovial Inflammation in Rheumatoid Arthritis. Med Sci Monit 2019;25:2246-56. doi: 10.12659/MSM.915451 [published Online First: 2019/03/28]

[2]Mun S, Lee J, Park A, et al. Proteomics Approach for the Discovery of Rheumatoid Arthritis Biomarkers Using Mass Spectrometry. Int J Mol Sci 2019;20(18) doi: 10.3390/ijms20184368 [published Online First: 2019/09/08]

[3]Zhu N, Hou J, Wu Y, et al. Identification of key genes in rheumatoid arthritis and osteoarthritis based on bioinformatics analysis. Medicine (Baltimore) 2018;97(22):e10997. doi: 10.1097/MD.0000000000010997 [published Online First: 2018/06/01]

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

AB0005 IDENTIFICATION OF KEY GENES AND PATHWAYS FOR PSORIASIS BASED ON GEO DATABASES BY BIOINFORMATICS ANALYSIS

Background:

Psoriasis is an immune-mediated, genetic disease manifesting in the skin or joints or both, and also has a strong genetic predisposition and autoimmune pathogenic traits1. The hallmark of psoriasis is sustained inflammation that leads to uncontrolled keratinocyte proliferation and dysfunctional differentiation. And it’s also a chronic relapsing disease, which often necessitates a long-term therapy2.

Objectives:

To investigate the molecular mechanisms of psoriasis and find the potential gene targets for diagnosis and treating psoriasis.

Methods:

Total 334 gene expression data of patients with psoriasis research (GSE13355 GSE14905 and GSE30999) were obtained from the Gene Expression Omnibus database. After data preprocessing and screening of differentially expressed genes (DEGs) by R software. Online toll Metascape3 was used to analyze Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis of DEGs. Interactions of proteins encoded by DEGs were discovered by Protein-protein interaction network (PPI) using STRING online software. Cytoscape software was utilized to visualize PPI and the degree of each DEGs was obtained by analyzing the topological structure of the PPI network.

Results:

A total of 611 DEGs were found to be differentially expressed in psoriasis. GO analysis revealed that up-regulated DEGs were mostly associated with defense and response to external stimulus while down-regulated DEGs were mostly associated with metabolism and synthesis of lipids. KEGG enrichment analysis suggested they were mainly enriched in IL-17 signaling, Toll-like receptor signaling and PPAR signaling pathways, Cytokine-cytokine receptor interaction and lipid metabolism. In addition, top 9 key genes (CXCL10, OASL, IFIT1, IFIT3, RSAD2, MX1, OAS1, IFI44 and OAS2) were identified through Cytoscape.

Conclusion:

DEGs of psoriasis may play an essential role in disease development and may be potential pathogeneses of psoriasis.

References:

[1]Boehncke WH, Schon MP. Psoriasis. Lancet 2015;386(9997):983-94. doi: 10.1016/S0140-6736(14)61909-7 [published Online First: 2015/05/31].

[2]Zhang YJ, Sun YZ, Gao XH, et al. Integrated bioinformatic analysis of differentially expressed genes and signaling pathways in plaque psoriasis. Mol Med Rep 2019;20(1):225-35. doi: 10.3892/mmr.2019.10241 [published Online First: 2019/05/23].

[3]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

POS0742 SCREENING AND BIOINFORMATICS ANALYSIS OF HUB GENES AND PATHWAYS FOR PRIMARY SJÖGREN’S SYNDROME BASED ON GEO DATABASE

Background:

Primary Sjögren’s syndrome (pSS) is an autoimmune disease that featured as lymphoplasmacytic infiltration of the exocrine glands leading to sicca symptoms1. However, its underlying molecular mechanisms remain elusive.

Objectives:

This study aims to identify differentially expressed genes (DEGs) and pathways associated with the progression of pSS using bioinformatics analysis and explore its pathogenesis.

Methods:

The pSS-associated gene chip data set GSE66795 was obtained from the Gene Expression Omnibus (GEO) database, which included 131 cases of fully-phenotyped pSS patients’ whole blood samples and 29 cases of control samples. DEGs were screened Using R software. Online tool Metascape2 was used to make Gene Ontology (GO) and KEGG pathway enrichment. The PPI network was performed using String database. Hub genes were identified by Cytoscape.

Results:

A total of 108 DEGs were captured, including 101 up-regulated genes and 7 down-regulated genes. GO enrichment showed that these DEGs were primarily enriched in defense response to virus, response to interferon-gamma, regulation of innate immune response, response to interferon-beta, double-stranded RNA binding, response to interferon-alpha. KEGG pathway enrichment analysis showed these DEGs were principally enriched in Influenza A, RIG-I-like receptor signaling pathway, necroptosis, Staphylococcus aureus infection. Finally, 9 hub genes (STAT1, IRF7, OAS2, GBP1, OAS1, IFIT3, IFIH1, OAS3, DDX60) had highest degree value.

Conclusion:

The findings identified molecular mechanisms and the key hub genes that may involve in the occurrence and development of pSS.

References:

[1]Francois H, Mariette X. Renal involvement in primary Sjogren syndrome. Nat Rev Nephrol 2016;12(2):82-93. doi: 10.1038/nrneph.2015.174 [published Online First: 2015/11/17].

[2]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

POS0848 IDENTIFICATION OF POTENTIAL CRUCIAL GENES AND KEY PATHWAYS IN PULMONARY ARTERIAL HYPERTENSION WITH SYSTEMIC SCLEROSIS BY BIOINFORMATIC ANALYSIS

Background:

Pulmonary arterial hypertension with systemic sclerosis (SSc-PAH) is the main cause of death in patients with SSc. Early diagnosis and timely treatment are very important to reduce the mortality of patients with SSc-PAH1. At present, there are not many sensitive markers for the diagnosis of SSc-PAH. Therefore, it is necessary to mine more sensitive markers as more accurate and practical predictors, which is of great significance for the diagnosis and treatment of SSc-PAH.

Objectives:

To discover the differentially expressed genes (DEGs) and activated signaling pathways in SSc-PAH.

Methods:

Fifty-five samples (27 SSc-PAH v.s 28 normal controls) in GSE33463 chip data obtained from Gene Expression Omnibus (GEO) were included in this study. DEGs in SSc-PAH patients were screened by R, key pathways and hub genes were discoved by Metascape2, STRING3 and Cytoscape.

Results:

Total 431 genes with large differences were identified, including 238 up-regulated genes and 193 down-regulated genes, after standardizing the data (|logFC| > 1; P < 0.05). GO analysis showed that the upregulated genes were mainly involved in defense response to virus, hemoglobin complex, platelet alpha granule membrane and cytokine binding. The downregulated genes were mainly characterized by positive regulation of cell death, regulation of MAPK cascade, regulation of DNA-binding transcription factor activity and transcription factor AP-1 complex. Several significant enriched pathways obtained in the KEGG pathway analysis were Influenza A, Hepatitis C, IL-17 signaling pathway, MAPK signaling pathway, Toll-like receptor signaling pathway. Finally, after the selected differential genes were introduced into STRING online software, the data information of protein interaction network was derived, and 12 core genes in the network were identified, they were CXCL8, PPBP, LPAR1, FPR2, GNG11, CXCL10, LPAR5, JUN, C3AR1, CCR2, CCR3, IRF2.

Conclusion:

The genes and signal pathways related to SSc-PAH discovered by bioinformatics methods could not only provided new molecular markers for its diagnosis and treatment, but also provided new ideas for its related biological research.

References:

[1]Zheng JN, Li Y, Yan YM, et al. Identification and Validation of Key Genes Associated With Systemic Sclerosis-Related Pulmonary Hypertension. Front Genet 2020;11:816. doi: 10.3389/fgene.2020.00816 [published Online First: 2020/08/15].

[2]Zhou Y, Zhou B, Pache L, et al. Metascape provides a biologist-oriented resource for the analysis of systems-level datasets. Nat Commun 2019;10(1):1523. doi: 10.1038/s41467-019-09234-6 [published Online First: 2019/04/05].

[3]Szklarczyk D, Gable AL, Lyon D, et al. STRING v11: protein-protein association networks with increased coverage, supporting functional discovery in genome-wide experimental datasets. Nucleic Acids Res 2019;47(D1):D607-D13. doi: 10.1093/nar/gky1131 [published Online First: 2018/11/27].

Acknowledgements:

This project was supported by National Science Foundation of China (82001740), Open Fund from the Key Laboratory of Cellular Physiology (Shanxi Medical University) (KLCP2019) and Innovation Plan for Postgraduate Education in Shanxi Province (2020BY078).

Disclosure of Interests:

None declared

Total genetic contribution assessment across the human genome

Quantifying the overall magnitude of every single locus' genetic effect on the widely measured human phenome is of great challenge. We introduce a unified modelling technique that can consistently provide a total genetic contribution assessment (TGCA) of a gene or genetic variant without thresholding genetic association signals. Genome-wide TGCA in five UK Biobank phenotype domains highlights loci such as the HLA locus for medical conditions, the bone mineral density locus WNT16 for physical measures, and the skin tanning locus MC1R and smoking behaviour locus CHRNA3 for lifestyle. Tissue-specificity investigation reveals several tissues associated with total genetic contributions, including the brain tissues for mental health. Such associations are driven by tissue-specific gene expressions, which share genetic basis with the total genetic contributions. TGCA can provide a genome-wide atlas for the overall genetic contributions in each particular domain of human complex traits.

[Contribution of sympathetic activation to antihypertrophic memory after regression of exercise-induced physiological myocardial hypertrophy in mice]

OBJECTIVE

To investigate whether anti-hypertrophic memory exists after regression of exercise-induced physiological myocardial hypertrophy (PMH) and explore the contribution of sympathetic activation to hypertrophic memory formation.

OBJECTIVE

Seventy-two mice were randomized equally into 6 groups, including sedentary sham-operated group, exercise hypertrophic preconditioning (EHP) + sham operation group, bisoprolol (an adrenergic β1 receptor blocker) + EHP + sham operation group (biso+Exe+Sham group), sedentary group with transverse aortic constriction (TAC) (Sed+TAC group), EHP+ TAC group (Exe+TAC group), and bisoprolol+EHP+TAC group (biso+Exe+TAC group). The mice in the EHP groups were subjected to 3 weeks of swimming training, and in the bisoprolol groups, bisoprolol was administered by gavage once daily from two days before till the end of the training. One week after the training, TAC or sham surgery was performed. Echocardiography and hemodynamic measurements were performed to evaluate cardiac function of the mice, and the myocardial tissues were examined histologically to detect cardiac remodeling.

OBJECTIVE

Compared with the sedentary group, the mice receiving 3 weeks of swimming training had significantly increased heart weight to body weight ratio (HW/BW), HW to tibia length ratio (HW/TL), and the cross-sectional area of the cardiomyocytes (P < 0.05). One week after the training, exercise-induced PMH rapidly diminished and both HW/BW and HW/TL recovered the baseline levels. Treatment with bisoprolol obviously prevented the occurrence of PMH. Four weeks after TAC, the left ventricular posterior wall thickness, HW/BW, HW/TL, left ventricular end diastolic pressure and cross-sectional area of cardiomyocytes were all significantly lower (P < 0.05) while the left ejection fraction and maximal change rate of left ventricular pressure were significantly higher (P < 0.05) in Exe + TAC group than in Sed + TAC group. No significant difference was found in these parameters between biso + Exe + TAC group and Sed + TAC group.

OBJECTIVE

Anti-hypertrophic memory exists even after the regression of exercise-induced PMH, which may be attributed to the activation of sympathetic nervous system during exercise.

The relationship between intestinal flora changes and osteoporosis in rats with inflammatory bowel disease and the improvement effect of probiotics

OBJECTIVE

The aim of this study was to investigate the relationship between the changes in intestinal flora and the occurrence of osteoporosis in rats with inflammatory bowel disease and the improvement effect of probiotics.

MATERIALS AND METHODS

A total of 100 Sprague Dawley (SD) model rats with colitis were selected as research objects. All rats were randomly divided into two groups, including: bowel disease group and osteoporosis group, with 50 rats in each group. Stool samples were collected from all rats, and Lactobacillus, Escherichia coli and Bifidobacteria were cultured and counted. The relationship between the occurrence of related osteoporosis and intestinal flora was analyzed as well. Thereafter, the rats in osteoporosis group were randomly divided into two subgroups, namely, control group (n=25) and observation group (n=25). Observation group was treated with probiotics by gastrogavage, while the control group was treated with the same volume of physiological saline. Next, the changes in serum osteoprotegerin (OPG), osteoprotegerin ligand [receptor activator of nuclear factor-kappa B ligand (RANKL)], procollagen type I carboxy-terminal propeptide (PICP), bone mineral density (BMD), bone alkaline phosphatase (BALP), tartrate-resistant acid phosphatase (TRACP), calcium concentration (Ca), and inflammatory cytokine levels were compared between the two groups after intervention.

RESULTS

Osteoporosis group had significantly more Escherichia coli and notably fewer Lactobacillus and Bifidobacteria than bowel disease group (p<0.05). Pearson correlation analysis revealed that the occurrence of osteoporosis in rats with inflammatory bowel disease was negatively correlated with the count of Escherichia coli, whereas was positively related to the counts of Lactobacillus and Bifidobacteria (p<0.05). Moreover, the levels of serum OPG, PICP, TRACP, and Ca in observation group were remarkably higher than those in the control group (p<0.05). However, the levels of serum RANKL, BALP, interleukin-6 (IL-6), tumor necrosis factor-alpha (TNF-α), and interferon-gamma (INF-γ) were markedly lower than those in the control group (p<0.05).

CONCLUSIONS

Osteoporosis in rats with inflammatory bowel disease has a negative association with the count of Escherichia coli, and a positive correlation with the counts of Lactobacillus and Bifidobacteria. In addition, treatment with probiotics can effectively alleviate osteoporosis symptoms in rats with inflammatory bowel disease by influencing the level of corresponding cytokines.

Accurate diagnosis of colorectal cancer based on histopathology images using artificial intelligence

BACKGROUND

Accurate and robust pathological image analysis for colorectal cancer (CRC) diagnosis is time-consuming and knowledge-intensive, but is essential for CRC patients' treatment. The current heavy workload of pathologists in clinics/hospitals may easily lead to unconscious misdiagnosis of CRC based on daily image analyses.

METHODS

Based on a state-of-the-art transfer-learned deep convolutional neural network in artificial intelligence (AI), we proposed a novel patch aggregation strategy for clinic CRC diagnosis using weakly labeled pathological whole-slide image (WSI) patches. This approach was trained and validated using an unprecedented and enormously large number of 170,099 patches, > 14,680 WSIs, from > 9631 subjects that covered diverse and representative clinical cases from multi-independent-sources across China, the USA, and Germany.

RESULTS

Our innovative AI tool consistently and nearly perfectly agreed with (average Kappa statistic 0.896) and even often better than most of the experienced expert pathologists when tested in diagnosing CRC WSIs from multicenters. The average area under the receiver operating characteristics curve (AUC) of AI was greater than that of the pathologists (0.988 vs 0.970) and achieved the best performance among the application of other AI methods to CRC diagnosis. Our AI-generated heatmap highlights the image regions of cancer tissue/cells.

CONCLUSIONS

This first-ever generalizable AI system can handle large amounts of WSIs consistently and robustly without potential bias due to fatigue commonly experienced by clinical pathologists. It will drastically alleviate the heavy clinical burden of daily pathology diagnosis and improve the treatment for CRC patients. This tool is generalizable to other cancer diagnosis based on image recognition.

Genetic mechanisms of critical illness in COVID-19

Host-mediated lung inflammation is present1, and drives mortality2, in the critical illness caused by coronavirus disease 2019 (COVID-19). Host genetic variants associated with critical illness may identify mechanistic targets for therapeutic development3. Here we report the results of the GenOMICC (Genetics Of Mortality In Critical Care) genome-wide association study in 2,244 critically ill patients with COVID-19 from 208 UK intensive care units. We have identified and replicated the following new genome-wide significant associations: on chromosome 12q24.13 (rs10735079, P = 1.65 × 10-8) in a gene cluster that encodes antiviral restriction enzyme activators (OAS1, OAS2 and OAS3); on chromosome 19p13.2 (rs74956615, P = 2.3 × 10-8) near the gene that encodes tyrosine kinase 2 (TYK2); on chromosome 19p13.3 (rs2109069, P = 3.98 ×  10-12) within the gene that encodes dipeptidyl peptidase 9 (DPP9); and on chromosome 21q22.1 (rs2236757, P = 4.99 × 10-8) in the interferon receptor gene IFNAR2. We identified potential targets for repurposing of licensed medications: using Mendelian randomization, we found evidence that low expression of IFNAR2, or high expression of TYK2, are associated with life-threatening disease; and transcriptome-wide association in lung tissue revealed that high expression of the monocyte-macrophage chemotactic receptor CCR2 is associated with severe COVID-19. Our results identify robust genetic signals relating to key host antiviral defence mechanisms and mediators of inflammatory organ damage in COVID-19. Both mechanisms may be amenable to targeted treatment with existing drugs. However, large-scale randomized clinical trials will be essential before any change to clinical practice.

Properties of Heavy Secondary Fluorine Cosmic Rays: Results from the Alpha Magnetic Spectrometer

Precise knowledge of the charge and rigidity dependence of the secondary cosmic ray fluxes and the secondary-to-primary flux ratios is essential in the understanding of cosmic ray propagation. We report the properties of heavy secondary cosmic ray fluorine F in the rigidity R range 2.15 GV to 2.9 TV based on 0.29 million events collected by the Alpha Magnetic Spectrometer experiment on the International Space Station. The fluorine spectrum deviates from a single power law above 200 GV. The heavier secondary-to-primary F/Si flux ratio rigidity dependence is distinctly different from the lighter B/O (or B/C) rigidity dependence. In particular, above 10 GV, the F/Si/B/O ratio can be described by a power law R^{δ} with δ=0.052±0.007. This shows that the propagation properties of heavy cosmic rays, from F to Si, are different from those of light cosmic rays, from He to O, and that the secondary cosmic rays have two classes.

Properties of Iron Primary Cosmic Rays: Results from the Alpha Magnetic Spectrometer

We report the observation of new properties of primary iron (Fe) cosmic rays in the rigidity range 2.65 GV to 3.0 TV with 0.62×10^{6} iron nuclei collected by the Alpha Magnetic Spectrometer experiment on the International Space Station. Above 80.5 GV the rigidity dependence of the cosmic ray Fe flux is identical to the rigidity dependence of the primary cosmic ray He, C, and O fluxes, with the Fe/O flux ratio being constant at 0.155±0.006. This shows that unexpectedly Fe and He, C, and O belong to the same class of primary cosmic rays which is different from the primary cosmic rays Ne, Mg, and Si class.

Variants of WNT7A and GPR124 are associated with hemorrhagic transformation following intravenous thrombolysis in ischemic stroke

AIMS

The canonical Wnt signaling pathway plays an essential role in blood-brain barrier integrity and intracerebral hemorrhage in preclinical stroke models. Here, we sought to explore the association between canonical Wnt signaling and hemorrhagic transformation (HT) following intravenous thrombolysis (IVT) in acute ischemic stroke (AIS) patients as well as to determine the underlying cellular mechanisms.

METHODS

355 consecutive AIS patients receiving IVT were included. Blood samples were collected on admission, and HT was detected at 24 hours after IVT. 117 single-nucleotide polymorphisms (SNPs) of 28 Wnt signaling genes and exon sequences of 4 core cerebrovascular Wnt signaling components (GPR124, RECK, FZD4, and CTNNB1) were determined using a customized sequencing chip. The impact of identified genetic variants was further studied in HEK 293T cells using cellular and biochemical assays.

RESULTS

During the study period, 80 patients experienced HT with 27 parenchymal hematoma (PH). Compared to the non-PH patients, WNT7A SNPs (rs2163910, P = .001, OR 2.727; rs1124480, P = .002, OR 2.404) and GPR124 SNPs (rs61738775, P = .012, OR 4.883; rs146016051, P < .001, OR 7.607; rs75336000, P = .044, OR 2.503) were selectively enriched in the PH patients. Interestingly, a missense variant of GPR124 (rs75336000, c.3587G>A) identified in the PH patients resulted in a single amino acid alteration (p.Cys1196Tyr) in the intracellular domain of GPR124. This variant substantially reduced the activity of WNT7B-induced canonical Wnt signaling by decreasing the ability of GPR124 to recruit cytoplasmic DVL1 to the cellular membrane.

CONCLUSION

Variants of WNT7A and GPR124 are associated with increased risk of PH in patients with AIS after intravenous thrombolysis, likely through regulating the activity of canonical Wnt signaling.

Updates on Clinical and Genetic Heterogeneity of ASPM in 12 Autosomal Recessive Primary Microcephaly Families in Pakistani Population

Microcephaly (MCPH) is a genetically heterogeneous disorder characterized by non-progressive intellectual disability, small head circumference, and small brain size compared with the age- and sex-matched population. MCPH manifests as an isolated condition or part of another clinical syndrome; so far, 25 genes have been linked with MCPH. Many of these genes are reported in Pakistani population, but due to a high rate of consanguinity, a significant proportion of MCPH cohort is yet to be explored. MCPH5 is the most frequently reported type, accounting for up to 68.75% alone in a genetically constrained population like Pakistan. In the current study, whole exome sequencing (WES) was performed on probands from 10 families sampled from South Waziristan and two families from rural areas of the Pakistani Punjab. Candidate variants were validated through Sanger sequencing in all available family members. Variant filtering and in silico analysis identified three known mutations in ASPM, a MCPH5-associated gene. The founder mutation p.Trp1326^* was segregating in 10 families, which further confirmed the evidence that it is the most prominent mutation in Pashtun ethnicity living in Pakistan and Afghanistan. Furthermore, the previously known mutations p.Arg3244^* and p.Arg1019^* were inherited in two families with Punjab ethnic profile. Collectively, this study added 12 more families to the mutational paradigm of ASPM and expanded the Pakistani MCPH cohort.

COX-2/PGE2 facilitates fracture healing by activating the Wnt/β-catenin signaling pathway

OBJECTIVE

The aim of this study was to explore the influence of cyclooxygenase-2 (COX-2)/prostaglandin E2 (PGE2) on fracture healing by activating the Wnt/β-catenin signaling pathway.

MATERIALS AND METHODS

In this study, 36 adult Sprague-Dawley (SD) rats raised in our laboratory were selected as research objects. The rats were subjected to fracture surgery on the middle part of the right femoral shaft. Subsequently, they were randomly divided into the control group and experimental groups (including experimental group A and experimental group B). Rats in experimental group A were injected with PGE 2 or COX-2 selective inhibitor NS-398, while rats in experimental group B were injected with PGE2 (5 μmol/L). Meanwhile, rats in the control group were injected with the same amount of normal saline. After that, the transcriptional levels of PEG2, COX-2, vascular endothelial growth factor (VEGF) and β-catenin in rats of the experimental group A, experimental group B and control group were detected via fluorescence quantitative Polymerase Chain Reaction (PCR) assay. Enzyme-linked immunosorbent assay (ELISA) and Western blotting were conducted to determine the changes in protein levels of PEG2, COX-2, VEGF and β-catenin in rats of the experimental group A, experimental group B and control group. The expression level of VEGF in bone tissues at fracture ends of rats in the experimental group A, experimental group B and control group was observed through the hematoxylin-eosin (HE) staining. Furthermore, micro-computed tomography (CT) was employed to evaluate callus formation.

RESULTS

The transcriptional and translational levels of COX-2, β-catenin and VEGF in rats of experimental group A treated with COX-2 inhibitors were significantly down-regulated when compared with those of the control group, showing statistically significant differences (p<0.05). However, the levels of these genes were markedly elevated in the experimental group B treated with PGE2 in comparison with those in the control group, and the differences were statistically significant (p<0.05). After 6 weeks, HE staining showed that the expression level of VEGF in rats of the experimental group B was remarkably higher than that of the experimental group A (p<0.05). Micro-CT results revealed that the mean trabecular plate density (MTPD) of rats in the experimental group B (73.29±5.4) was markedly higher than the number of osteoblasts (49.6±3.9) in the experimental group A, showing a statistically significant difference (p<0.05).

CONCLUSIONS

COX-2/PGE2 facilitates fracture healing by activating the Wnt/β-catenin signaling pathway.