Identification of banana ADA1 gene family members and their expression profiles under biotic and abiotic stresses / 生物工程学报

The Spt-Ada-Gcn5-acetyltransferase (SAGA) is an ancillary transcription initiation complex which is highly conserved. The ADA1 (alteration/deficiency in activation 1, also called histone H2A functional interactor 1, HFI1) is a subunit in the core module of the SAGA protein complex. ADA1 plays an important role in plant growth and development as well as stress resistance. In this paper, we performed genome-wide identification of banana ADA1 gene family members based on banana genomic data, and analyzed the basic physicochemical properties, evolutionary relationships, selection pressure, promoter cis-acting elements, and its expression profiles under biotic and abiotic stresses. The results showed that there were 10, 6, and 7 family members in Musa acuminata, Musa balbisiana and Musa itinerans. The members were all unstable and hydrophilic proteins, and only contained the conservative SAGA-Tad1 domain. Both MaADA1 and MbADA1 have interactive relationship with Sgf11 (SAGA-associated factor 11) of core module in SAGA. Phylogenetic analysis revealed that banana ADA1 gene family members could be divided into 3 classes. The evolution of ADA1 gene family members was mostly influenced by purifying selection. There were large differences among the gene structure of banana ADA1 gene family members. ADA1 gene family members contained plenty of hormonal elements. MaADA1-1 may play a prominent role in the resistance of banana to cold stress, while MaADA1 may respond to the Panama disease of banana. In conclusion, this study suggested ADA1 gene family members are highly conserved in banana, and may respond to biotic and abiotic stress.

Genome-wide association analysis of agronomic traits related to eggplant fruits: a review / 生物工程学报

Eggplant is an important horticultural crop and one of the most widely grown vegetables in the Solanaceae family. Eggplant fruit-related agronomic traits are complex quantitative traits with low efficiency and long cycle time for traditional breeding selection. With the rapid development of high-throughput sequencing technology and bioinformatics tools, genome-wide association study (GWAS) has shown great application potential in analyzing the genetic rules of complex agronomic traits related to eggplant fruits. This paper first reviews the progress of genome-wide association analysis in eggplant fruit shape, fruit color and other fruit-related agronomic traits. Subsequently, aiming at the problem of missing heritability, which is common in the genetic studies of eggplant quantitative traits, this paper puts forward the development strategies of eggplant GWAS in the future based on the hot spots of application of four GWAS strategies in the research of agronomics traits related to eggplant fruits. Lastly, the application of GWAS strategy in the field of eggplant molecular breeding is expected to provide a theoretical basis and reference for the future use of GWAS to analyze the genetic basis of various eggplant fruit-related traits and to select fruit materials that meet consumer needs.

Application of Mendelian randomization in liver cancer / 临床肝胆病杂志

In recent years， the research method of Mendelian randomization based on genome-wide association studies has been widely used for etiological exploration in the medical field， which can effectively overcome the confounding biases and interference of reverse causalities in traditional observational researches with its unique advantages of the distributive randomness and timing priority of genetic variants. This article reviews the method of Mendelian randomization and its application in liver cancer， in order to provide new ideas for the research on causal association in liver cancer.

Bidirectional casual effects between periodontitis and Sjögren's syndrome: a Mendelian randomization study / 口腔疾病防治

Objective@#To evaluate the bidirectional association between periodontitis and Sjögren's syndrome using the Mendelian randomization (MR) method.@*Methods@#Genome-wide association study (GWAS) data of periodontitis (N = 45 563) and Sjögren's syndrome (N = 214 435) were selected to meet the requirements of the same ethnicity and different regions. Inverse variance-weighted (IVW), MR-Egger, and weighted median (WM) tests were used to evaluate the causal effect. Cochran's Q statistics, MR-Egger intercept, MR-PRESSO and leave-one-out analysis were used as sensitivity analyses to assess the stability and reliability of the results.@*Results@#After screening, the GWAS data of Sjögren's syndrome were based on the Finnish region, and the periodontitis GWAS data were based on the UK region, both of which originated from European ancestry. Using IVW (OR = 1.017, 95% CI = 0.956-1.082), MR-Egger (OR = 0.985, 95% CI= 0.956-1.082), and WM (OR =1.021, 95% CI = 0.948-1.099), no causal effect of Sjögren's syndrome on periodontitis was found using any of the three methods. Conversely, no causal effect of periodontitis on Sjögren's syndrome was found (IVW, OR = 1.024, 95% CI = 0.852-1.230; MR-Egger, OR = 0.978, 95% CI = 0.789-1.212; WM, OR = 1.024, 95% CI = 0.846-1.260). The sensitivity analyses indicated that the results were stable and reliable. Cochran's Q test and MR-PRESSO revealed that there was no significant heterogeneity among the instrumental variables, which included single nucleotide polymorphisms (SNPs). The intercept of MR-Egger regression indicated no pleiotropy in the included SNPs. No individual SNP was found that significantly affected the results using the leave-one-out method.@*Conclusion@#This study does not support a bidirectional causal effect between periodontitis and Sjögren's syndrome.

Recurrent Quantification Analysis Based Study of Wide-Field Calcium Imaging Data in Relation to Brain's Wake/Sleep Condition

Wide-Field Calcium Images (WFCI) directly reflect neuronal excitation, but their poor frame rate could be a drawback for time series analysis. This work was aimed at exploring the diagnostic capability retained by a time series obtained from calcium imaging data. To that purpose, we analyzed publicly available data from 2.88 hour continuous recordings of calcium images obtained from seven mice at different wake/sleep stages. Data were obtained from the Physionet portal and were submitted to Recurrence Quantification Analysis (RQA). The association between retrosplenial and parietal areas was also assessed. Nonlinear RQA analysis allowed to identify the right retrosplenial and parietal areas as particularly sensitive to changes in sleep walking condition. Specifically, our results suggested that the RQA feature lmean decreases in non-REM sleep_1 stage as compared to waking stage. Sleep (both sleep_1 stage and REM) apparently elicits an increase in the association between retrosplenial and parietal areas. Overall, these results suggest that RQA and association analysis are appropriate to assess modifications associated to changes in brain condition, in spite of the low sampling rate of WFCI signals.

Las Imágenes de Calcio de Campo Ancho (Wide-Field Calcium Images, WFCI) reflejan directamente la excitación neuronal, pero su escasa resolución temporal pudiera resultar un impedimento para el análisis de series temporales. El presente trabajo tuvo por finalidad explorar la capacidad diagnostica que retiene una serie temporal extraída de imágenes de calcio. Para ello, se estudió una base de datos disponible en la red que contiene registros de 2.88 horas de duración de imágenes de calcio correspondientes a 7 ratones transgénicos a diferentes estadios de sueño/vigilia. Los datos fueron descargados del portal Physionet y sometidos a Análisis de Cuantificación Recurrente (Recurrent Quantification Analysis, RQA). La asociación entre las áreas retrosplenial y parietal derechas fue también evaluada. El análisis no lineal mediante RQA permitió identificar las áreas retrosplenial y parietal derechas como zonas particularmente sensibles a cambios en el estado de sueño/vigilia. Específicamente, nuestros resultados sugieren que el índice l mean se redujo en el estadio 1 de sueño no REM en comparación con el estado de vigilia. El estado de sueño, tanto REM como no-REM aparentemente induce un reforzamiento en la apreciación entre las áreas retrosplenial y parietal derechas. En su conjunto, estos resultados apuntan que el análisis de RQA y de asociación entre áreas son pertinentes para sensar las modificaciones asociadas a cambios en el estado del cerebro, a pesar de la baja resolución temporal de las señales WFCI.

Topographic distribution of retinal neovascularization in proliferative diabetic retinopathy using ultra-wide field angiography

Purpose: To analyze the topographic distribution of neovascularization (NV) and capillary nonperfusion (CNP) using ultra?wide field fluorescein angiography (UWFFA) in patients with proliferative diabetic retinopathy (PDR). Methods: This was a prospective, single?center, observational study in which all patients who presented between March 2019 and December 2020 and satisfied the inclusion criteria were recruited. In our study, patients with treatment?naïve PDR without any fibrovascular proliferation underwent UWFFA. The images were analyzed qualitatively for the topographic distribution of NV and the CNP area was quantified. The number of lesions picked by UWFFA was compared with 7 standard field (7SF) image using overlay of 7SF. The main outcome measure was characteristics of neovascularization, such as the number, location, and area of CNP, measured using UWFFA, which was considered with 95% confidence intervals (CI). Results: Two hundred and fifty?three eyes of 187 patients with a mean age of 56.03 ± 8 years were included. Mean neovascularization elsewhere (NVE) was 2.91 ± 3.43. Maximum NVEs were seen in the superotemporal (ST; 0.9 ± 1.13) quadrant, followed by the inferotemporal (IT; 0.7 ± 1.08), inferonasal (IN; 0.66 ± 1.02) and superonasal (SN; 0.66 ± 1.01) quadrants. Maximum CNP area was seen in the SN (13.75 ± 8.83 disc diameter square [DD2]) quadrant, followed by the IN (13.48 ± 8.59 DD2), IT (11.34 ± 8.37 DD2), and ST (11.3 ± 8.34 DD2) quadrants. Mean CNP area was maximum in patients with only neovascularization of disc (NVD; 64.99 ± 41.47 DD2), followed by both NVD and NVE (61.37 ± 35.61 DD2), and was minimum in patients with only NVE (36.44 ± 22.03 DD2). Eighty?one (32%) eyes out of 253 had NVE and 189 (75%) out of 253 had CNP area outside 7SF (overlay) of Early Treatment Diabetic Retinopathy Study (ETDRS). Conclusion: Diabetic NV lesions and CNP areas are distributed asymmetrically throughout the retina and are not restricted to the posterior pole. Compared to conventional 7SF imaging, UWFFA reveals significantly more retinal vascular pathology in patients with PDR.

Exploration on the Medical Ethics Education Path of "Combining Moral and Technical Education" of Vocational Medical Students under the Concept of "Three-wide Education" / 中国医学伦理学

The educational purpose of "three-wide education" is in line with the overall goal of talent cultivation in colleges and universities, and fits the development laws of ideological and political work in colleges and universities in the new era. It is an important measure to leverage the joint efforts of education and improve the quality of education. Under the concept of "three-wide education", medical ethics education in higher vocational medical colleges lacks systematization and big data support, medical students’ "knowing morality" and "conducting morality" are not unified, the content of medical ethics teaching is outdated, and teaching methods are single, which is inconsistent with students’ innovative cognitive thinking and derailed from clinical and social real needs, making it difficult to arouse students’ interest in learning. Against the backdrop of continuously improving professional literacy requirements for medical students, this paper explored the medical ethics education path of "combining moral and technical education" for vocational medical students under the concept of "three-wide education", and formed training paths such as "three integration of medical ethics, three progressions of knowledge and action", the coordinated education of ideological and political courses and ideological and political education in the course, the "trinity" of school, family, and society, the innovative multi-dimensional medical ethics education teaching methods, the construction of a medical ethics practice platform, and the establishment of medical ethics cultural education data management platforms, with a view to providing reference ideas for the cultivation of medical ethics among vocational medical students.

Exploration and Practice of Constructing the Ideological and Political Work System in Colleges and Universities of Traditional Chinese Medicine: Taking Shaanxi University of Chinese Medicine as an Example / 中国医学伦理学

The foundation of the university lies in the cultivation of virtue and people. The construction of the ideological and political work system in Traditional Chinese Medicine (TCM) colleges and universities embodies the Marxist on the theory of all-sided development of human beings, the concept and practical requirements of "three-wide education", and the special laws of the ideological and political work in TCM colleges and universities. It is the realistic need to carry out the strategy of cultivating good quality, to innovate and develop the system of ideological and political work, and to improve the quality of TCM personnel training. TCM Colleges and universities should dig deeply into the ideological and political elements of TCM resources, integrate "virtue establishment and people cultivation" into the whole process of talent training, actively explore new ideas, new ways and new methods of constructing the ideological and political work system of TCM colleges and universities, and strive to cultivate high-quality TCM talents who shoulder the task of national rejuvenation.

Screening of pathogenic molecular markers of Staphylococcus aureus in children based on whole genome sequencing technology / 中国当代儿科杂志

OBJECTIVES@#To explore the molecular characteristics of Staphylococcus aureus (S. aureus) in children, and to compare the molecular characteristics of different types of strains (infection and colonization strains) so as to reveal pathogenic molecular markers of S. aureus.@*METHODS@#A cross-sectional study design was used to conduct nasopharyngeal swab sampling from healthy children in the community and clinical samples from infected children in the hospital. Whole genome sequencing was used to detect antibiotic resistance genes and virulence genes. A random forest method to used to screen pathogenic markers.@*RESULTS@#A total of 512 S. aureus strains were detected, including 272 infection strains and 240 colonization strains. For virulence genes, the carrying rates of enterotoxin genes (seb and sep), extracellular enzyme coding genes (splA, splB, splE and edinC), leukocytotoxin genes (lukD, lukE, lukF-PV and lukS-PV) and epidermal exfoliating genes (eta and etb) in infection strains were higher than those in colonization strains. But the carrying rates of enterotoxin genes (sec, sec3, seg, seh, sei, sel, sem, sen, seo and seu) were lower in infection strains than in colonization strains (P<0.05). For antibiotic resistance genes, the carrying rates of lnuA, lnuG, aadD, tetK and dfrG were significantly higher in infection strains than in colonization strains (P<0.05). The accuracy of cross-validation of the random forest model for screening pathogenic markers of S. aureus before and after screening was 69% and 68%, respectively, and the area under the curve was 0.75 and 0.70, respectively. The random forest model finally screened out 16 pathogenic markers (sem, etb, splE, sep, ser, mecA, lnuA, sea, blaZ, cat(pC233), blaTEm-1A, aph(3')-III, ermB, ermA, ant(9)-Ia and ant(6)-Ia). The top five variables in the variable importance ranking were sem (OR=0.40), etb (OR=3.95), splE (OR=1.68), sep (OR=3.97), and ser (OR=1.68).@*CONCLUSIONS@#The random forest model can screen out pathogenic markers of S. aureus and exhibits a superior predictive performance, providing genetic evidence for tracing highly pathogenic S. aureus and conducting precise targeted interventions.

Research progress on fundus examination methods and fundus image characteristics of retinopathy of prematurity / 国际眼科杂志(Guoji Yanke Zazhi)

Retinopathy of prematurity(ROP)is the primary cause of preventable childhood blindness. It is hard to screen, diagnose and objectively evaluate. There are various modalities for ROP screening, including various contact or non-contact imaging devices, smart phone-based fundus photography, and artificial intelligence-based fundus image analysis. The diagnosis of ROP is based on visualization and recording of the entire retinal fundus of ROP, which is also the basis for subsequent screening, treatment assessment. Fundus screening is critical for early recognition and facilitates early detection and prompt referral. Potential features may be found by analyzing and summarizing the characteristics of ROP fundus images. Subsequently, timely and targeted ROP prevention and treatment could be performed. Artificial intelligence promotes automatic, quantifiable and objective diagnosis of ROP. This article reviews commonly used clinical fundus examination methods and fundus image characteristics of ROP and summarizes the latest research progress on the application of artificial intelligence in the automatic diagnosis of ROP.

Kinome-wide polypharmacology profiling of small molecules by multi-task graph isomorphism network approach

Prediction of the interactions between small molecules and their targets play important roles in various applications of drug development, such as lead discovery, drug repurposing and elucidation of potential drug side effects. Therefore, a variety of machine learning-based models have been developed to predict these interactions. In this study, a model called auxiliary multi-task graph isomorphism network with uncertainty weighting (AMGU) was developed to predict the inhibitory activities of small molecules against 204 different kinases based on the multi-task Graph Isomorphism Network (MT-GIN) with the auxiliary learning and uncertainty weighting strategy. The calculation results illustrate that the AMGU model outperformed the descriptor-based models and state-of-the-art graph neural networks (GNN) models on the internal test set. Furthermore, it also exhibited much better performance on two external test sets, suggesting that the AMGU model has enhanced generalizability due to its great transfer learning capacity. Then, a naïve model-agnostic interpretable method for GNN called edges masking was devised to explain the underlying predictive mechanisms, and the consistency of the interpretability results for 5 typical epidermal growth factor receptor (EGFR) inhibitors with their structure‒activity relationships could be observed. Finally, a free online web server called KIP was developed to predict the kinome-wide polypharmacology effects of small molecules (http://cadd.zju.edu.cn/kip).

Clinical application of Neuroform Atlas stent-assisted coiling in the treatment of unruptured wide-neck intracranial aneurysms / 北京大学学报(医学版)

OBJECTIVE@#To assess the safety and efficacy of Neuroform Atlas stent used in treatment of unruptured wide-neck intracranial aneurysms.@*METHODS@#Clinical data of 62 patients with unruptured wide-neck intracranial aneurysms undergoing Neuroform Atlas stent-assisted coiling from August 2020 to September 2021 were retrospectively analyzed. There were 64 aneurysms in those 62 patients. Among them, 25 aneurysms were located at the bifurcation of M1 segment on middle cerebral artery, 16 at the anterior communicating artery, 10 at the C7 segment of internal carotid artery, 5 at the C6 segment of internal carotid artery, 4 at the apex of basilar artery, 3 at the A3 segment of anterior cerebral artery, and 1 at the M2 segment of middle cerebral artery. All the patients underwent Neuroform Atlas stent-assisted coiling, including 49 patients with single stent assisted coiling and 15 patients with dual stents assisted coiling (14"Y"style and 1"X"style). After the procedure, the immediate DSA was performed to evaluate the status of aneurysm occlusion and the parent artery patency. The clinical follow-up was performed 3 months after the operation and evaluated based on the modified Rankin Scale(mRS).DSA image was reviewed at 6 months after operation and Raymond grading scale was used to assess the status of aneurysm occlusion and the parent artery patency.@*RESULTS@#A total of 62 patients with 64 aneurysms were all achieved technical success(100%).The immediate post-procedural Raymond scale was assessed, including Raymond Ⅰ in 57 aneurysms(89.1%, 57/64), Raymond Ⅱ in 6 aneurysms(9.3%, 6/64) and Raymond Ⅲ in 1 aneurysm(1.6%, 1/64). The peri-procedural complications rate was 4.8%(3/62), 2 patients developed intraoperative thrombosis and 1 patient suffered from local subarachnoid hemorrhage. Among them, 55 patients obtained 3 months clinical follow-up after operation and all the patients had good outcomes (mRS≤2), 50 patients with 52 aneurysms were followed up with DSA 6 months after operation, including Raymond Ⅰ in 45 aneurysms(86.5%, 45/52), Raymond Ⅱ in 4 aneurysms(7.7%, 4/52) and Raymond Ⅲ in 3 aneurysms(5.8%, 3/52).@*CONCLUSION@#Neuroform Atlas stent for the treatment of unruptured wide-neck intracranial aneurysms has high safety and good efficacy, and has its advantages over other traditional stents.

Research progress on wide-field multimodal image of peripheral retinal degeneration / 国际眼科杂志(Guoji Yanke Zazhi)

Peripheral retinal degeneration is a typical lesion in ophthalmic clinical practice. Each type of degeneration affects distinct retinal layers and may lead to sight-threatening complications. Due to its specific location, where current ophthalmic imaging technologies have difficulties observing, the pathogenesis remains unclear despite previous works. This review outlines the characteristics of peripheral retinal degeneration by different wide-field imaging technologies, including ultra-wide field fundus imaging, wide field spectral domain optical coherence tomography, optical coherence tomography angiography and fundus fluorescein angiography, as well as new perspectives on their pathogenesis or pathological characteristics so as to provide new ideas for clinical diagnosis and management. Due to the small size of sample and the lack of prospective and long-term observation of multimodal imaging, it is still impossible to comprehensively evaluate the progression and risk of different types of degeneration. Therefore, it is expected that wide-field multimodal imaging technology will be more widely applied to study the mechanism of peripheral retinal degeneration and guide the clinical practice options.

Molecular characterization of mutations associated with resistance among 72 multidrug-resistant strains of Mycobacterium tuberculosis by whole genome sequencing / 中国热带医学

@#Abstract: Objective　To understand the characteristics of mutations associated with resistance among 72 multidrug-resistant tuberculosis (MDR-TB) strains using whole genome sequencing (WGS) and to evaluate the performance of WGS for predicting MDR-TB drug resistance. Methods　The clinical strains isolated from patients who visited the outpatient department of Tianjin Center for Tuberculosis Control from January to September in 2020 were collected. Identification tests using p-nitrobenzoic acid (PNB) medium were performed. Drug susceptibility tests (proportion method) on L-J medium were performed. After excluding duplicate strains, 72 MDR-TB strains were selected for WGS. Data were analyzed by using online databases and the phenotypic drug susceptibility test results were compared with resistance profiles predicted by WGS. Results　All of 72 MDR-TB strains belonged to linage 2, and there was no significant difference in rate of pre-extensive drug-resistant tuberculosis (pre-XDR-TB) between modern type and ancestral type (χ2=0.287, P=0.592). A total of 81 mutation types were found from resistance-related genes for 12 anti-tuberculosis drugs, and the common mutation types in different drug-resistant strains were: streptomycin (SM): rpsL Lys43Arg; isoniazid (INH): katG Ser315Thr; rifampicin (RIF): rpoB Ser450Leu; ethambutol (EMB): embB Met306Val; ofloxacin (OFX), levofloxacin (LFX), moxifloxacin (MFX): gyrA Asp94Gly; kanamycin (KAM), capreomycin (CAP), amikacin (AMK): rrs 1401a>g; para-aminosalicylic acid (PAS): folC Ile43Thr. Nine mutation types were found in 9 prothionamide (PTO)-resistant strains, one type for each strain. The sensitivity and specificity of WGS for predicting resistance to different drugs were SM: 98.15% and 88.89%, INH: 90.28% and -, RIF: 98.62% and -, EMB: 79.49% and75.76%, OFX: 97.30% and 85.71%, KAM: 85.71% and 98.46%, PAS: 27.27% and 95.08%, PTO: 81.82% and 60.66%, CAP: 60.00% and 98.51%, LFX: 97.22% and 83.33%, MFX: 97.30% and 85.71%, AMK:100.00% and 100.00%, respectively. Conclusion　WGS is a rapid and promising method which has high consistency with the phenotypic drug sensitivity test. Therefore, it has good application prospects in predicting drug resistance in MDR-TB.

Genome-wide DNA methylation and transcriptome expression profiles of peripheral blood mononuclear cells in patients with systemic sclerosis with interstitial lung disease / 中南大学学报(医学版)

OBJECTIVES@#This study aims to investigate the genome-wide DNA methylation and transcriptome expression profiles of peripheral blood mononuclear cells (PBMCs) in patients with systemic sclerosis (SSc) with interstitial lung disease (ILD), and to analyze the effects of DNA methylation on Wnt/β-catenin and chemokine signaling pathways.@*METHODS@#PBMCs were collected from 19 patients with SSc (SSc group) and 18 healthy persons (control group). Among SSc patients, there were 10 patients with ILD (SSc with ILD subgroup) and 9 patients without ILD (SSc without ILD subgroup). The genome-wide DNA methylation and gene expression level were analyzed by using Illumina 450K methylation chip and Illumina HT-12 v4.0 gene expression profiling chip. The effect of DNA methylation on Wnt/β-catenin and chemokine signal pathways was investigated.@*RESULTS@#Genome-wide DNA methylation analysis identified 71 hypermethylated CpG sites and 98 hypomethylated CpG sites in the SSc with ILD subgroup compared with the SSc without ILD subgroup. Transcriptome analysis distinguished 164 upregulated genes and 191 downregulated genes in the SSc with ILD subgroup as compared with the SSc without ILD subgroup. In PBMCs of the SSc group, 35 genes in Wnt/β-catenin signaling pathway were hypomethylated, while frizzled-1 (FZD1), mitogen-activated protein kinase 9 (MAPK9), mothers against DPP homolog 2 (SMAD2), transcription factor 7-like 2 (TCF7L2), and wingless-type MMTV integration site family, member 5B (WNT5B) mRNA expressions were upregulated as compared with the control group (all P<0.05). Compared with the SSc without ILD subgroup, the mRNA expressions of dickkopf homolog 2 (DKK2), FZD1, MAPK9 were upregulated in the SSc with ILD subgroup, but the differences were not statistically significant (all P>0.05). In PBMCs of the SSc group, 38 genes in chemokine signaling pathway were hypomethylated, while β-arrestin 1 (ARRB1), C-X-C motif chemokine ligand 10 (CXCL10), C-X-C motif chemokine ligand 16 (CXCL16), FGR, and neutrophil cytosolic factor 1C (NCF1C) mRNA expressions were upregulated as compared with the control group (all P<0.05). Compared with the SSc without ILD subgroup, the mRNA expressions of ARRB1, CXCL10, CXCL16 were upregulated in the SSc with ILD subgroup, but the differences were not statistically significant (all P>0.05).@*CONCLUSIONS@#There are differences in DNA methylation and transcriptome profiles between SSc with ILD and SSc without ILD. The expression levels of multiple genes in Wnt/β- catenin and chemokine signaling pathways are upregulated, which might be associatea with the pathogenesis of SSc.

How data science and AI-based technologies impact genomics

Advancements in high-throughput sequencing have yielded vast amounts of genomic data, which are studied using genome-wide association study (GWAS)/phenome-wide association study (PheWAS) methods to identify associations between the genotype and phenotype. The associated findings have contributed to pharmacogenomics and improved clinical decision support at the point of care in many healthcare systems. However, the accumulation of genomic data from sequencing and clinical data from electronic health records (EHRs) poses significant challenges for data scientists. Following the rise of artificial intelligence (AI) technology such as machine learning and deep learning, an increasing number of GWAS/PheWAS studies have successfully leveraged this technology to overcome the aforementioned challenges. In this review, we focus on the application of data science and AI technology in three areas, including risk prediction and identification of causal single-nucleotide polymorphisms, EHR-based phenotyping and CRISPR guide RNA design. Additionally, we highlight a few emerging AI technologies, such as transfer learning and multi-view learning, which will or have started to benefit genomic studies.

Association of ticagrelor with risk of infection：a two-sample Mendelian randomization study based on the GWAS database / 中国药房

OBJECTIVE To investigate the causal association between ticagrelor and risk of infection METHODS Two-sample Mendelian randomization was adopted. Genetic instrumental variables were selected based on the results of the largest genome-wide association analysis to in vivo exposure of ticagrelor and its major active metabolite AR-C124910XX. The causal associations of ticagrelor and its major active metabolite AR-C124910XX with drug indications （coronary artery disease， unstable angina pectoris， myocardial infarction， stroke and ischemic stroke）were analyzed by inverse variance weighted Mendelian randomization model as a positive control for genetic instrumental variables. The causal relationship between ticagrelor and bacterial infection， acute lower respiratory infection， bacterial pneumoniae， pneumoniae，acute upper respiratory infection and sepsis were furtheranalyzed by using this method， and the robustness of the results was assessed by using heterogeneity tests and horizontal 202002030415） pleiotropy tests. RESULTS The increase of area under the curve at steady state （AUCss） of the genetic surrogated ticagrelor significantly reduced the risk of coronary artery disease， myocardial infarction and unstable angina pectoris （P＜0.001）. AUCss genetic instrument variables of its main active metabolite AR-C124910XX failed to pass positive control. Further analysis showed that the increase of the genetic surrogated ticagrelor exposure suggestively reduced the risk of bacterial infection [OR（95%CI）＝0.80（0.65，0.99），P＝0.040] and sepsis [OR （95%CI）＝0.84（0.73， 0.98）， P＝0.023]. The results of the heterogeneity tests showed that there was no heterogeneity in the causal association of the genetic surrogated ticagrelor AUCss with bacterial infection and sepsis （P＞0.05）. The results of horizontal pleiotropy tests showed that the causal association of genetic surrogated ticagrelor AUCss with bacterial infection and sepsis had no effects on horizontal pleiotropy （P＞0.05）. CONCLUSIONS Ticagrelor has a potential role in reducing the risk of sepsis and bacterial infections.

Association between gut microbiome and intracerebral hemorrhage based on genome-wide association study data / 中南大学学报(医学版)

OBJECTIVES@#Intracerebral hemorrhage (ICH) has the highest mortality and disability rates among various subtypes of stroke. Previous studies have shown that the gut microbiome (GM) is closely related to the risk factors and pathological basis of ICH. This study aims to explore the causal effect of GM on ICH and the potential mechanisms.@*METHODS@#Genome wide association study (GWAS) data on GM and ICH were obtained from Microbiome Genome and International Stroke Genetics Consortium. Based on the GWAS data, we first performed Mendelian randomization (MR) analysis to evaluate the causal association between GM and ICH. Then, a conditional false discovery rate (cFDR) method was conducted to identify the pleiotropic variants.@*RESULTS@#MR analysis showed that Pasteurellales, Pasteurellaceae, and Haemophilus were negatively correlated with the risk of ICH, whileVerrucomicrobiae, Verrucomicrobiales, Verrucomicrobiaceae, Akkermansia, Holdemanella, and LachnospiraceaeUCG010 were positively correlated with ICH. By applying the cFDR method, 3 pleiotropic loci (rs331083, rs4315115, and rs12553325) were found to be associated with both GM and ICH.@*CONCLUSIONS@#There is a causal association and pleiotropic variants between GM and ICH.

Isolation and genome-wide evolutionary analysis of a type Ⅲ WU polyomavirus strain / 中华微生物学和免疫学杂志

Objective:To isolate and culture WU polyomavirus (WUPyV), and to analyze the genome-wide evolutionary patterns, homology and population dynamics.Methods:Real-time quantitative PCR was used to detect the nasopharyngeal aspirate samples of hospitalized children with respiratory tract infection in Beijing Friendship Hospital during 2020 to 2022. Primary human airway epithelial cells cultured at the air-liquid interface were used to isolate and culture WUPyV. Whole genome sequence of the isolated strain was obtained by Sanger sequencing. For phylogenetic and evolutionary dynamics analysis, the whole genome was compared with the published whole genome sequences in GenBank database.Results:The detection rate of WUPyV was 4.7% (31/659) during 2020 to 2022, and a clinical strain BJ0593 of WUPyV type Ⅲc was successfully isolated. The homology of the whole genome and gene fragments of WUPyV was high. The average evolutionary rate of VP2 gene was about 1.256×10 -4 substitution/site every year, and the population dynamics of WUPyV tended to be flat in the last decade. Conclusions:This study successfully isolated a clinical WUPyV type Ⅲ strain for the first time, which provided the basis for further investigation on the molecular evolution and pathogenicity of WUPyV.

Association between exonic polymorphisms of human leukocyte antigen-G gene and non-segmental vitiligo in the Korean population

Background: Vitiligo is a pigmentary skin disorder characterised by a chronic and progressive loss of melanocytes. Although several theories have been suggested to the pathogenesis of vitiligo, an autoimmune process leading to melanocyte destruction appears most likely. Human leukocyte antigen-G is a non-classic, major histocompatibility complex Class I molecule that plays an important role in the suppression of the immune response. Several recent studies have provided evidences that polymorphisms in the human leukocyte antigen-G gene might be related with autoimmune diseases. Objectives: The aim of this study was to decide whether exonic single nucleotide polymorphisms in human leukocyte antigen-G contribute to the risk of developing non-segmental vitiligo in the Korean population. Methods: To evaluate the associations between exonic single nucleotide polymorphisms (rs1630223 [Ala5Ala] and rs12722477 [Leu134Ile]) of human leukocyte antigen-G and vitiligo, 244 patients with vitiligo and 398 healthy controls were recruited. Genotyping was performed using Fluidigm 192.24 Dynamic Array with EP1 (Fluidigm Corp., CA). The SNP type assay (Fluidigm Corp., CA), which employs allele-specifically designed fluorescences (FAM or VIC) primers and a common reverse primer was applied and the data were analysed using the EP1 single nucleotide polymorphisms genotyping analysis software to obtain genotype calls. Results: Two exonic single nucleotide polymorphisms (rs1630223 and rs12722477) exhibited significant associations with susceptibility and remained a statistically significant association following Bonferroni correction. These two single nucleotide polymorphisms were located within a block of linkage disequilibrium. Haplotypes G-C and A-A comprising rs1630223 and rs12722477 demonstrated a significant association with non-segmental vitiligo. Limitations: The protein expression level of patients with vitiligo and controls was not studied and a replication study of the genetic association in an independent group was not managed. Conclusion: Our results suggest that exonic human leukocyte antigen-G polymorphisms (rs1630223 and rs12722477) are associated with the development of non-segmental vitiligo.