Generation of a human haploid neural stem cell line for genome-wide genetic screening

BACKGROUND Haploid embryonic stem cells(haESCs)have been established in many species.Differentiated haploid cell line types in mammals are lacking due to spontaneous diploidization during differentiation that compromises lineage-specific screens.AIM To derive human haploid neural stem cells(haNSCs)to carry out lineage-specific screens.METHODS Human haNSCs were differentiated from human extended haESCs with the help of Y27632(ROCK signaling pathway inhibitor)and a series of cytokines to reduce diploidization.Neuronal differentiation of haNSCs was performed to examine their neural differentiation potency.Global gene expression analysis was conducted to compare haNSCs with diploid NSCs and haESCs.Fluorescence activated cell sorting was performed to assess the diploidization rate of extended haESCs and haNSCs.Genetic manipulation and screening were utilized to evaluate the significance of human haNSCs as genetic screening tools.RESULTS Human haESCs in extended pluripotent culture medium showed more compact and smaller colonies,a higher efficiency in neural differentiation,a higher cell survival ratio and higher stability in haploidy maintenance.These characteristics effectively facilitated the derivation of human haNSCs.These human haNSCs can be generated by differentiation and maintain haploidy and multipotency to neurons and glia in the long term in vitro.After PiggyBac transfection,there were multiple insertion sites in the human haNSCs’genome,and the insertion sites were evenly spread across all chromosomes.In addition,after the cells were treated with manganese,we were able to generate a list of manganese-induced toxicity genes,demonstrating their utility as genetic screening tools.CONCLUSION This is the first report of a generated human haploid somatic cell line with a complete genome,proliferative ability and neural differentiation potential that provides cell resources for recessive inheritance and drug targeted screening.

Genome-wide screening of long non-coding RNAs involved in rubber biosynthesis in Eucommia ulmoides

Increasing evidence indicates that long non- coding RNAs （IncRNAs） play pivotal roles in regulatory networks controlling plant and animal gene expression. However, IncRNA roles in regulating rubber biosynthesis in Eucommia ulmoides, an emerging source of natural rubber （Eu-rubber）, are currently unknown. Here, we report on RNA deep-sequencing of E. ulmoides fruits at two developmental stages. Based on application of a stringent pipeline, 29,1o3 IncRNAs and 9,048 transcripts of uncertain coding potential （TUCPs） were identified.Two differentially expressed （DE）TUCPs appear to simultaneously regulate 12 protein-coding genes involved in Eu-rubber biosynthesis （GIEBs）, as well as 95 DE genes. Functional categorization of these 95 DE genes indicated their involvement in subcellular microstructures and cellular processes, such as cell wall, cell division, and growth. These DE genes may participate in the differentiation and development of laticifers, where Eu-rubber is synthesized. A model is proposed in which ＂commanders＂ （DE TUCPs） direct the ＂builders＂ （DE genes） to construct a ＂storehouse＂ of materials needed for Eu-rubber synthesis, and the ＂workers＂ （GIEBs） to synthesize Eu-rubber. These findings provide insights into both cis- and trans-polyisoprene biosynthesis in plants, laying the foundation for additional studies of this crucial process.

Colorectal cancer screening:A review of current knowledge and progress in research

Colorectal cancer(CRC)is one of the most prevalent malignancies worldwide,being the third most commonly diagnosed malignancy and the second leading cause of cancer-related deaths globally.Despite the progress in screening,early diagnosis,and treatment,approximately 20%-25%of CRC patients still present with metastatic disease at the time of their initial diagnosis.Furthermore,the burden of disease is still expected to increase,especially in individuals younger than 50 years old,among whom early-onset CRC incidence has been increasing.Screening and early detection are pivotal to improve CRC-related outcomes.It is well established that CRC screening not only reduces incidence,but also decreases deaths from CRC.Diverse screening strategies have proven effective in decreasing both CRC incidence and mortality,though variations in efficacy have been reported across the literature.However,uncertainties persist regarding the optimal screening method,age intervals and periodicity.Moreover,adherence to CRC screening remains globally low.In recent years,emerging technologies,notably artificial intelligence,and non-invasive biomarkers,have been developed to overcome these barriers.However,controversy exists over the actual impact of some of the new discoveries on CRC-related outcomes and how to effectively integrate them into daily practice.In this review,we aim to cover the current evidence surrounding CRC screening.We will further critically assess novel approaches under investigation,in an effort to differentiate promising inno-vations from mere novelties.

Esophageal cancer screening,early detection and treatment:Current insights and future directions

Esophageal cancer ranks among the most prevalent malignant tumors globally,primarily due to its highly aggressive nature and poor survival rates.According to the 2020 global cancer statistics,there were approximately 604000 new cases of esophageal cancer,resulting in 544000 deaths.The 5-year survival rate hovers around a mere 15%-25%.Notably,distinct variations exist in the risk factors associated with the two primary histological types,influencing their worldwide incidence and distribution.Squamous cell carcinoma displays a high incidence in specific regions,such as certain areas in China,where it meets the cost-effect-iveness criteria for widespread endoscopy-based early diagnosis within the local population.Conversely,adenocarcinoma(EAC)represents the most common histological subtype of esophageal cancer in Europe and the United States.The role of early diagnosis in cases of EAC originating from Barrett's esophagus(BE)remains a subject of controversy.The effectiveness of early detection for EAC,particularly those arising from BE,continues to be a debated topic.The variations in how early-stage esophageal carcinoma is treated in different regions are largely due to the differing rates of early-stage cancer diagnoses.In areas with higher incidences,such as China and Japan,early diagnosis is more common,which has led to the advancement of endoscopic methods as definitive treatments.These techniques have demonstrated remarkable efficacy with minimal complications while preserving esophageal functionality.Early screening,prompt diagnosis,and timely treatment are key strategies that can significantly lower both the occurrence and death rates associated with esophageal cancer.

Development and validation of a prediction model for early screening of people at high risk for colorectal cancer

BACKGROUND Colorectal cancer(CRC)is a serious threat worldwide.Although early screening is suggested to be the most effective method to prevent and control CRC,the current situation of early screening for CRC is still not optimistic.In China,the incidence of CRC in the Yangtze River Delta region is increasing dramatically,but few studies have been conducted.Therefore,it is necessary to develop a simple and efficient early screening model for CRC.AIM To develop and validate an early-screening nomogram model to identify individuals at high risk of CRC.METHODS Data of 64448 participants obtained from Ningbo Hospital,China between 2014 and 2017 were retrospectively analyzed.The cohort comprised 64448 individuals,of which,530 were excluded due to missing or incorrect data.Of 63918,7607(11.9%)individuals were considered to be high risk for CRC,and 56311(88.1%)were not.The participants were randomly allocated to a training set(44743)or validation set(19175).The discriminatory ability,predictive accuracy,and clinical utility of the model were evaluated by constructing and analyzing receiver operating characteristic(ROC)curves and calibration curves and by decision curve analysis.Finally,the model was validated internally using a bootstrap resampling technique.RESULTS Seven variables,including demographic,lifestyle,and family history information,were examined.Multifactorial logistic regression analysis revealed that age[odds ratio(OR):1.03,95%confidence interval(CI):1.02-1.03,P<0.001],body mass index(BMI)(OR:1.07,95%CI:1.06-1.08,P<0.001),waist circumference(WC)(OR:1.03,95%CI:1.02-1.03 P<0.001),lifestyle(OR:0.45,95%CI:0.42-0.48,P<0.001),and family history(OR:4.28,95%CI:4.04-4.54,P<0.001)were the most significant predictors of high-risk CRC.Healthy lifestyle was a protective factor,whereas family history was the most significant risk factor.The area under the curve was 0.734(95%CI:0.723-0.745)for the final validation set ROC curve and 0.735(95%CI:0.728-0.742)for the training set ROC curve.The calibration curve demonstrated a high correlation between the CRC high-risk population predicted by the nomogram model and the actual CRC high-risk population.CONCLUSION The early-screening nomogram model for CRC prediction in high-risk populations developed in this study based on age,BMI,WC,lifestyle,and family history exhibited high accuracy.

Non-participation of asymptomatic candidates in screening protocols reduces early diagnosis and worsens prognosis of colorectal cancer

The Agatsuma et al’s study shows that despite the evidence of the benefits of an early colorectal cancer(CRC)diagnosis,through screening in asymptomatic subjects,up to 50%of candidates reject this option and many of those affected are diagnosed later,in advanced stages.The efficacy of screening programs has been well-established for several years,which reduces the risk of CRC morbidity and mortality,without taking into account the test used for screening,or other tools.Nevertheless,a significant proportion of patients remain unscreened,so understanding the factors involved,as well as the barriers of the population to adherence is the first step to possibly modify the participation rate.These barriers could include a full range of social and political aspects,especially the type of financial provision of each health service.In Japan,health services are universal,and this advantageous situation makes it easier for citizens to access to these services,contributing to the detection of various diseases,including CRC.Interestingly,the symptomatic CRC group had a lower early-stage diagnosis rate than the patients detected during follow-up for other comorbidities,and symptomatic and cancer screening groups showed similar early-stage diagnosis.

Genetic screening of liver cancer:State of the art

Liver cancer,primarily hepatocellular carcinoma,remains a global health challenge with rising incidence and limited therapeutic options.Genetic factors play a pivotal role in the development and progression of liver cancer.This state-of-the-art paper provides a comprehensive review of the current landscape of genetic screening strategies for liver cancer.We discuss the genetic underpinnings of liver cancer,emphasizing the critical role of risk-associated genetic variants,somatic mutations,and epigenetic alterations.We also explore the intricate interplay between environmental factors and genetics,highlighting how genetic screening can aid in risk stratification and early detection via using liquid biopsy,and advancements in high-throughput sequencing technologies.By synthesizing the latest research findings,we aim to provide a comprehensive overview of the state-of-the-art genetic screening methods for liver cancer,shedding light on their potential to revolutionize early detection,risk assessment,and targeted therapies in the fight against this devastating disease.

Assessing the conservation impact of Chinese indigenous chicken populations between ex-situ and in-situ using genome-wide SNPs

Conservation programs require rigorous evaluation to ensure the preservation of genetic diversity and viability of conservation populations. In this study, we conducted a comparative analysis of two indigenous Chinese chicken breeds, Gushi and Xichuan black-bone, using whole-genome SNPs to understand their genetic diversity, track changes over time and population structure. The breeds were divided into five conservation populations(GS1, 2010, ex-situ;GS2, 2019, ex-situ;GS3, 2019, in-situ;XB1, 2010, in-situ;and XB2, 2019, in-situ) based on conservation methods and generations. The genetic diversity indices of three conservation populations of Gushi chicken showed consistent trends, with the GS3 population under in-situ strategy having the highest diversity and GS2 under ex-situ strategy having the lowest. The degree of inbreeding of GS2 was higher than that of GS1 and GS3. Conserved populations of Xichuan black-bone chicken showed no obvious changes in genetic diversity between XB1 and XB2. In terms of population structure, the GS3 population were stratified relative to GS1 and GS2. According to the conservation priority, GS3 had the highest contribution to the total gene and allelic diversity in GS breed, whereas the contribution of XB1 and XB2 were similar. We also observed that the genetic diversity of GS2 was lower than GS3, which were from the same generation but under different conservation programs(in-situ and ex-situ). While XB1 and XB2 had similar levels of genetic diversity. Overall, our findings suggested that the conservation programs performed in ex-situ could slow down the occurrence of inbreeding events, but could not entirely prevent the loss of genetic diversity when the conserved population size was small, while in-situ conservation populations with large population size could maintain a relative high level of genetic diversity.

Reliability of a computerized system for strabismus screening

AIM:To evaluate the reliability of Photo-Hirschberg screening for global strabismus performed by non-specialized personnel.METHODS:Participants at three sites were enrolled.One person at each site was trained in visual acuity measurement and use of the computerized system.Visual acuity was measured,and strabismus testing was performed using two flash photographs.All data from the three primary observers were sent to an experienced assistant researcher,who was blinded to the primary results,for re-evaluation.The primary and re-evaluation results of the Photo-Hirschberg screenings using weighted kappa for agreement were compared.RESULTS:The study included 181 participants(88 males and 93 females)and the results for primary and re-evaluation screenings were corresponded.Ten participants with contrasting results presented with unclear corneal light reflex.Sensitivity and specificity were 100%[95%confidence interval(CI):29.0%-100%]and 99.4%(95%CI:96.6%-100%),respectively,based on the Agresti test of the primary evaluation,considering the re-evaluated classification as true.CONCLUSION:The computerized system can be used for primary strabismus screening by non-specialized personnel,with 98.8%agreement with specialists.However,it cannot be used as a substitute for professional examination.

Colorectal cancer screening: Modalities and adherence

In the last decade,several studies have explored various modalities and strategies for colorectal cancer(CRC)screening,taking into account epidemiological data,individual characteristics,and socioeconomic factors.In this editorial,we comment further on a retrospective study by Agatsuma et al published in the recent issue of the World Journal of Gastroenterology.Our focus is on screening trends,particularly in relation to efforts to improve the currently suboptimal uptake among the general population worldwide,aiming to enhance early diagnosis rates of CRC.There is a need to raise awareness through health edu-cation programs and to consider the use of readily available,non-invasive screening methods.These strategies are crucial for attracting screen-eligible populations to participate in first-line screening,especially those in high-or average-risk groups and in regions with limited resources.Liquid biopsies and biomarkers represent rapidly evolving trends in screening and diagnosis;however,their clinical relevance has yet to be standardized.

Epistasis-aware genome-wide association studies provide insights into the efficient breeding of high-yield and high-quality rice

Marker-assisted selection(MAS)and genomic selection(GS)breeding have greatly improved the efficiency of rice breeding.Due to the influences of epistasis and gene pleiotropy,ensuring the actual breeding effect of MAS and GS is still a difficult challenge to overcome.In this study,113 indica rice varieties(V)and their 565 testcross hybrids(TC)were used as the materials to investigate the genetic basis of 12 quality traits and nine agronomic traits.The original traits and general combining ability of the parents,as well as the original traits and midparent heterosis of TC,were subjected to genome-wide association analysis.In total,381 primary significantly associated loci(SAL)and 1,759 secondary SALs that had epistatic interactions with these primary SALs were detected.Among these loci,322 candidate genes located within or nearby the SALs were screened,204 of which were cloned genes.A total of 39 MAS molecular modules that are beneficial for trait improvement were identified by pyramiding the superior haplotypes of candidate genes and desirable epistatic alleles of the secondary SALs.All the SALs were used to construct genetic networks,in which 91 pleiotropic loci were investigated.Additionally,we estimated the accuracy of genomic prediction in the parent V and TC by incorporating either no SALs,primary SALs,secondary SALs or epistatic effect SALs as covariates.Although the prediction accuracies of the four models were generally not significantly different in the TC dataset,the incorporation of primary SALs,secondary SALs,and epistatic effect SALs significantly improved the prediction accuracies of 5(26%),3(16%),and 11(58%)traits in the V dataset,respectively.These results suggested that SALs and epistatic effect SALs identified based on an additive genotype can provide considerable predictive power for the parental lines.They also provide insights into the genetic basis of complex traits and valuable information for molecular breeding in rice.

Optimization of colorectal cancer screening strategies: New insights

In this editorial,we discuss the article by Agatsuma et al.We concentrate specifically on the current routinely used screening tests recommended by society guidelines and delve into the significance of early diagnosis of colorectal cancer(CRC)and its substantial impact on both incidence and mortality rates.Screening is highly recommended,and an early diagnosis stands out as the most crucial predictor of survival for CRC patients.Therefore,it is essential to identify and address the barriers hindering adherence to screening measures,as these barriers can vary among different populations.Furthermore,we focus on screening strategy optimization by selecting high-risk groups.Patients with comorbidities who regularly visit hospitals have been diagnosed at an early stage,showing no significant difference compared to patients undergoing regular screening.This finding highlights the importance of extending screening measures to include patients with comorbidities who do not routinely visit the hospital.

Leveraging the potential of big genomic and phenotypic data for genome-wide association mapping in wheat

Genome-wide association mapping studies(GWAS)based on Big Data are a potential approach to improve marker-assisted selection in plant breeding.The number of available phenotypic and genomic data sets in which medium-sized populations of several hundred individuals have been studied is rapidly increasing.Combining these data and using them in GWAS could increase both the power of QTL discovery and the accuracy of estimation of underlying genetic effects,but is hindered by data heterogeneity and lack of interoperability.In this study,we used genomic and phenotypic data sets,focusing on Central European winter wheat populations evaluated for heading date.We explored strategies for integrating these data and subsequently the resulting potential for GWAS.Establishing interoperability between data sets was greatly aided by some overlapping genotypes and a linear relationship between the different phenotyping protocols,resulting in high quality integrated phenotypic data.In this context,genomic prediction proved to be a suitable tool to study relevance of interactions between genotypes and experimental series,which was low in our case.Contrary to expectations,fewer associations between markers and traits were found in the larger combined data than in the individual experimental series.However,the predictive power based on the marker-trait associations of the integrated data set was higher across data sets.Therefore,the results show that the integration of medium-sized to Big Data is an approach to increase the power to detect QTL in GWAS.The results encourage further efforts to standardize and share data in the plant breeding community.

Screening, Treatment and Control of High Blood Pressure on Five Sites in Mali

Introduction: High blood pressure is defined as blood pressure greater than or equal to 140 mm Hg for systolic and or 90 mm Hg for diastolic. It constitutes a major public health problem, the leading chronic disease in the world. The objective was to determine the prevalence, treatment rate and control of hypertension. Methods: This was a cross-sectional and descriptive study which took place over a period of 6 months in a hospital environment and in the general population. Results: Of the 1000 participants, 637 had hypertension, giving a prevalence of 63.70% with a female predominance. Thirty-three percent (33%) were unaware of their high blood pressure. The age group 60 and more was the most represented (44%). A proportion of 33 and 23.20 were overweight and obese participants, respectively. Male subjects were more overweight than female, unlike obesity which was more common among female subjects. Sixty-two percent (62%) of hypertensives were treated, of whom 44% were non-compliant. The excessively high cost and consumption of medications as needed were the main factors in therapeutic non-compliance. Twenty-two percent (22%) of all hypertensive patients and 35% of treated hypertensive patients were controlled. Women were more treated but less observant and less controlled than men. Therapeutic coverage and combination therapy rates were lower in rural areas. Hypertensives who had a high level of education were better treated and controlled than those who had no level. Conclusion: High blood pressure remains a real public health problem in Mali. It is more common in people aged 60 and over and in females. One in three hypertensives were unaware of their hypertension. The majority received antihypertensive treatments, but only a minority of them had their hypertension controlled.

Genome-Wide Association Study of Cooked Rice Textural Attributes and Starch Physicochemical Properties in indica Rice

Rice cooking and eating qualities(CEQ)are mainly determined by cooked rice textural parameters and starch physicochemical properties.However,the genetic bases of grain texture and starch properties in rice have not been fully understood.We conducted a genome-wide association study for apparent amylose content(AAC),starch pasting viscosities,and cooked rice textural parameters using 279 indica rice accessions from the 3000 Rice Genome Project.We identified 26 QTLs in the whole population and detected single nucleotide polymorphisms(SNPs)with the lowest P-value at the Waxy(Wx)locus for all traits except pasting temperature and cohesiveness.Additionally,we detected significant SNPs at the SUBSTANDARD STARCH GRAIN6(SSG6)locus for AAC,setback(SB),hardness,adhesiveness,chewiness(CHEW),gumminess(GUM),and resilience.We subsequently divided the population using a SNP adjacent to the Waxy locus,and identified 23 QTLs and 12 QTLs in two sub-panels,WxT and WxA,respectively.In these sub-panels,SSG6 was also identified to be associated with pasting parameters,including peak viscosity,hot paste viscosity,cold paste viscosity,and consistency viscosity.Furthermore,a candidate gene encoding monosaccharide transporter 5(OsMST5)was identified to be associated with AAC,breakdown,SB,CHEW,and GUM.In total,39 QTLs were co-localized with known genes or previously reported QTLs.These identified genes and QTLs provide valuable information for genetic manipulation to improve rice CEQ.

Genome-wide association study of seedling nitrogen-use efficiency-associated traits in common wheat(Triticum aestivum L.)

Nitrogen(N)fertilizer application is essential for crop-plant growth and development.Identifying genetic loci associated with N-use efficiency(NUE)could increase wheat yields and reduce environmental pollution caused by overfertilization.We subjected a panel of 389 wheat accessions to N and chlorate(a nitrate analog)treatments to identify quantitative trait loci(QTL)controlling NUE-associated traits at the wheat seedling stage.Genotyping the panel with a 660K single-nucleotide polymorphism(SNP)array,we identified 397 SNPs associated with N-sensitivity index and chlorate inhibition rate.These SNPs were merged into 49 QTL,of which eight were multi-environment stable QTL and 27 were located near previously reported QTL.A set of 135 candidate genes near the 49 QTL included TaBOX(F-box family protein)and TaERF(ethylene-responsive transcription factor).A Tabox mutant was more sensitive to low-N stress than the wild-type plant.We developed two functional markers for Hap 1,the favorable allele of TaBOX.

Consensus on rapid screening for prodromal Alzheimer's disease in China

Alzheimer's disease(AD)is a common cause of dementia,characterised by cerebral amyloid-βdeposition,pathological tau and neurodegeneration.The prodromal stage of AD(pAD)refers to patients with mild cognitive impairment(MCl)and evidence of AD's pathology.At this stage,disease-modifying interventions should be used to prevent the progression to dementia.Given the inherent heterogeneity of MCl,more specific biomarkers are needed to elucidate the underlying AD's pathology.Although the uses of cerebrospinal fluid and positron emission tomography are widely accepted methods for detecting AD's pathology,their clinical applications are limited by their high costs and invasiveness,particularly in low-income areas in China.Therefore,to improve the early detection of Alzheimer's disease(AD)pathology through cost-effective screening methods,a panel of 45neurologists,psychiatrists andgerontologistswas invited to establish a formal consensus on the screening of pAD in China.The supportive evidence and grades of recommendations are based on a systematic literature review andfocus group discussion.National meetings were held to allow participants to review,vote and provide their expert opinions to reach a consensus.A majority(two-thirds)decision was used for questions for which consensus could not be reached.Recommended screening methods are presented in this publication,including neuropsychological assessment,peripheral biomarkers and brain imaging.In addition,a general workflow for Screening pAD in China is established,which will help clinicians identify individuals at high risk and determine therapeutic targets.

Evidence for the Reliability and Validity of the Arabic Version of the Student Risk Screening Scale for Internalizing and Externalizing Behaviors (SRSS-IE)

School-based universal screening for behavioral/emotional risk is a necessary first step to providing services in an educational setting for students with emotional and behavioral disorders (EBDs). Psychometric properties are critical to making decisions about choosing a screening instrument. The purpose of the present study was to examine the psychometric properties of the student risk screening scale for internalizing and externalizing behaviors (SRSS-IE). Participants included 3145 students and their teachers. Item-level analyses of the current sample supported the retention of all items. The internal consistency of the SRSS items ranged from 0.83 to 0.85. Convergent validity between the SRSS-IE and a well-established screening tool, the strength and difficulties questionnaire (SDQ), was found for the total score (r = 0.70). Additionally, the results of this study demonstrate strong social validity, suggesting the SRSS-IE to be a useful and functional screening tool. We conclude that the SRSS-IE is a valid and reliable instrument for assessing the level of emotional and behavioral difficulties among elementary students.

Genome-wide association mapping and genomic prediction of stalk rot in two mid-altitude tropical maize populations

Maize stalk rot reduces grain yield and quality.Information about the genetics of resistance to maize stalk rot could help breeders design effective breeding strategies for the trait.Genomic prediction may be a more effective breeding strategy for stalk-rot resistance than marker-assisted selection.We performed a genome-wide association study(GWAS)and genomic prediction of resistance in testcross hybrids of 677 inbred lines from the Tuxpe?o and non-Tuxpe?o heterotic pools grown in three environments and genotyped with 200,681 single-nucleotide polymorphisms(SNPs).Eighteen SNPs associated with stalk rot shared genomic regions with gene families previously associated with plant biotic and abiotic responses.More favorable SNP haplotypes traced to tropical than to temperate progenitors of the inbred lines.Incorporating genotype-by-environment(G×E)interaction increased genomic prediction accuracy.

Refining the targeted population and achieving better for colorectal cancer screening

This editorial comments on the article entitled“Stage at diagnosis of colorectal cancer through diagnostic route:Who should be screened?”by Agatsuma et al,who conducted a retrospective study aiming at clarifying the stage at colorectal cancer(CRC)diagnosis based on different diagnostic routes.We share our opinion about CRC screening programs.The current situation suggests the need for a more specific and targeted population for CRC screening.