Prenatal ultrasonography and genetic analysis of fetal cleidocranial dysplasia:A case report

BACKGROUND Cleidocranial dysplasia(CCD)is an infrequent clinical condition with an autosomal dominant inheritance pattern.It is characterized by abnormal clavicles,patent sutures and fontanelles,supernumerary teeth,and short stature.Approximately 60%-70%of patients with CCD have mutations in the RUNX family transcription factor 2 gene.However,prenatal diagnosis of CCD is difficult when the family history is unknown.CASE SUMMARY We report a rare case of fetal CCD with an unknown family history,confirmed by prenatal ultrasonography and genetic testing at a gestational age of 16 weeks.The genetic reports indicated that the fetus carried pathogenic mutations in the RUNX family transcription factor 2 gene(c.674G>A).After careful consideration,the pregnant woman and her family decided to continue the pregnancy.CONCLUSION Definitive prenatal diagnosis of CCD should include family history,ultrasound diagnosis,and genetic analysis,especially if family history is unknown.

Genetic insights in infectious diseases:Insights from a case report and implications for personalized medicine

The relationship between genetics and infectious diseases is important in shaping our understanding of disease susceptibility,progression,and treatment.Recent research shows the impact of genetic variations,such as heme-oxygenase promoter length,on diseases like malaria and sepsis,revealing both protective and inconclusive effects.Studies on vaccine responses highlight genetic markers like human leukocyte antigens,emphasizing the potential for personalized immunization strategies.The ongoing battle against drug-resistant tuberculosis(TB)illustrates the complexity of genomic variants in predicting resistance,highlighting the need for integrated diagnostic tools.Additionally,genome-wide association studies reveal antibiotic resistance mechanisms in bacterial genomes,while host genetic polymorphisms,such as those in solute carrier family 11 member 1 and vitamin D receptor,demonstrate their role in TB susceptibility.Advanced techniques like metagenomic next-generation sequencing promise detailed pathogen detection but face challenges in cost and accessibility.A case report involving a highly virulent Mycobacterium TB strain with the pks1 gene further highlights the need for genetic insights in understanding disease severity and developing targeted interventions.This evolving landscape emphasizes the role of genetics in infectious diseases,while also addressing the need for standardized studies and accessible technologies.

The genetic basis and improvement of photosynthesis in tomato

Photosynthesis is one the most important chemical reaction in plants,and it is the ultimate energy source of any living organisms.The light and dark reactions are two essential phases of photosynthesis.Light reaction harvests light energy to synthesize ATP and NADPH through an electron transport chain,and as well as giving out O_(2);dark reaction fixes CO_(2) into six carbon sugars by utilizing NADPH and energy from ATP.Subsequently,plants convert optical energy into chemical energy for maintaining growth and development through absorbing light energy.Here,firstly,we highlighted the biological importance of photosynthesis,and hormones and metabolites,photosynthetic and regulating enzymes,and signaling components that collectively regulate photosynthesis in tomato.Next,we reviewed the advances in tomato photosynthesis,including two aspects of genetic basis and genetic improvement.Numerous genes regulating tomato photosynthesis are gradually uncovered,and the interaction network among those genes remains to be constructed.Finally,the photosynthesis occurring in fruit of tomato and the relationship between photosynthesis in leaf and fruit were discussed.Leaves and fruits are photosynthate sources and sinks of tomato respectively,and interaction between photosynthesis in leaf and fruit exists.Additionally,future perspectives that needs to be addressed on tomato photosynthesis were proposed.

Genetic factors that predict response and failure of biologic therapy in inflammatory bowel disease

Inflammatory bowel disease(IBD)represents a significant disease burden marked by chronic inflammation and complications that adversely affect patients’quality of life.Effective diagnostic strategies involve clinical assessments,endoscopic evaluations,imaging studies,and biomarker testing,where early diagnosis is essential for effective management and prevention of long-term complications,highlighting the need for continual advancements in diagnostic methods.The intricate interplay between genetic factors and the outcomes of biological therapy is of critical importance.Unraveling the genetic determinants that influence responses and failures to biological therapy holds significant promise for optimizing treatment strategies for patients with IBD on biologics.Through an indepth examination of current literature,this review article synthesizes critical genetic markers associated with therapeutic efficacy and resistance in IBD.Understanding these genetic actors paves the way for personalized approaches,informing clinicians on predicting,tailoring,and enhancing the effectiveness of biological therapies for improved outcomes in patients with IBD.

GATIS score:An innovative prognostic score for rectal neuroendocrine neoplasms

In this article,we discussed the article by Zeng et al,published in a recent issue of the World Journal of Gastroenterology.The publication represents a significant advancement in the prognostic evaluation of rectal neuroendocrine neoplasms.The GATIS score is a single nomogram model that incorporates five key progno-stic factors:Tumor grade;T stage;tumor size;age;and the prognostic nutritional index.This innovation optimizes the prognostic process,delivering more accurate predictions of overall survival and progression-free survival compared to tradi-tional TNM staging and World Health Organization classification systems.The findings of the study were based on a retrospective analysis spanning 12 years and involving 1408 patients from 17 reference centers in China.In this editorial,we specifically examined the strengths and limitations of the study,the clinical implications of the GATIS score,and the questions arising from its conclusions.

The genetics of pediatric inflammatory bowel disease:Towards precision medicine

Pediatric inflammatory bowel disease(IBD)is a chronic and heterogeneous disease.IBD is commonly classified into Crohn’s disease and ulcerative colitis.It is linked to serious symptoms and complications.The onset of IBD commonly occurs during adolescence.Despite the significant number of cases globally(~5 million),the causes of pediatric IBD,which constitutes 25%of IBD patients,are not yet fully understood.Apart from environmental factors,genetic factors contribute to a higher risk of developing IBD.The predisposition risk of IBD can be investigated using genetic testing.Genetic mechanisms of pediatric IBD are highly complex which resulted in difficulty in selecting effective treatment or patient management.Genetic variation of IBD would serve as a basis for precision medicine and allow for the discovery of more robust treatment avenues for this condition in pediatric patients.This review aims to discuss the genetics of pediatric IBD,and current development in the screening,diagnosis,and treatment based on genetic profiling of pediatric IBD subjects toward more personalized management of this disease.

The collaborative cross mouse for studying the effect of host genetic background on memory impairments due to obesity and diabetes

Background:Over the past few decades,a threefold increase in obesity and type 2 diabetes(T2D)has placed a heavy burden on the health-care system and society.Previous studies have shown correlations between obesity,T2D,and neurodegenera-tive diseases,including dementia.It is imperative to further understand the relation-ship between obesity,T2D,and cognitive deficits.Methods:This investigation tested and evaluated the cognitive impact of obesity and T2D induced by high-fat diet(HFD)and the effect of the host genetic background on the severity of cognitive decline caused by obesity and T2D in collaborative cross(CC)mice.The CC mice are a genetically diverse panel derived from eight inbred strains.Results:Our findings demonstrated significant variations in the recorded phenotypes across different CC lines compared to the reference mouse line,C57BL/6J.CC037 line exhibited a substantial increase in body weight on HFD,whereas line CC005 ex-hibited differing responses based on sex.Glucose tolerance tests revealed significant variations,with some lines like CC005 showing a marked increase in area under the curve(AUC)values on HFD.Organ weights,including brain,spleen,liver,and kidney,varied significantly among the lines and sexes in response to HFD.Behavioral tests using the Morris water maze indicated that cognitive performance was differentially affected by diet and genetic background.Conclusions:Our study establishes a foundation for future quantitative trait loci map-ping using CC lines and identifying genes underlying the comorbidity of Alzheimer's disease(AD),caused by obesity and T2D.The genetic components may offer new tools for early prediction and prevention.

Genetic diversity and population genetic structure of Paeonia suffruticosa by chloroplast DNA simple sequence repeats(cpSSRs)

Paeonia suffruticosa Andr.is an endemic shrub flower in China with 2n=10.This study used 228 cultivars from four populations,i.e.,Jiangnan,Japan,Northwest,and Zhongyuan,as materials to explore the genetic diversity levels among different populations of tree peony varieties.The results showed that 34 bands were amplified using five pairs of cp SSR primers,with an average of 6.8 bands per primer pair.The average number of different alleles(N_(a)),effective alleles(N_(e)),Shannon's information index(I),diversity(H),and polymorphic information content(PIC)were 3.600,2.053,0.708,0.433,and 0.388,respectively.The PIC value was between 0.250 and 0.500,indicating a moderate level of polymorphism for the five cp SSR primer pairs.The genetic diversity levels of peony cultivars varied among different populations,with the Northwest population showing relatively lower levels(I=0.590,H=0.289,and PIC=0.263).A total of 52 haplotypes were identified in the four examined populations,and the number of haplotypes per population ranged from 11 to 22.Forty-four private haplotypes were detected across populations,and the Northwest population exhibiting the highest count of private haplotypes with 17.The mean number of effective number of haplotypes(N_(eh)),haplotypic richness(R_h),and diversity(H)were 8.351,6.824,and 0.893,respectively.Analysis of molecular variance indicated that genetic variation within tree peony germplasm was greater than that between germplasm resources,and the main variation was found within individuals of peony germplasm.Cluster analysis,principal coordinate analysis,and genetic structure analysis classified tree peonies from different origins into two groups,indicating a certain degree of genetic differentiation among these four tree peony cultivation groups.This study provides a theoretical basis for the exploration,utilization,and conservation of peony germplasm resources,as well as for research on the breeding of excellent varieties.

GATIS score for predicting the prognosis of rectal neuroendocrine neoplasms:A Chinese multicenter study of 12-year experience

BACKGROUND There is currently a shortage of accurate,efficient,and precise predictive instruments for rectal neuroendocrine neoplasms(NENs).AIM To develop a predictive model for individuals with rectal NENs(R-NENs)using data from a large cohort.METHODS Data from patients with primary R-NENs were retrospectively collected from 17 large-scale referral medical centers in China.Random forest and Cox proportional hazard models were used to identify the risk factors for overall survival and progression-free survival,and two nomograms were constructed.RESULTS A total of 1408 patients with R-NENs were included.Tumor grade,T stage,tumor size,age,and a prognostic nutritional index were important risk factors for prognosis.The GATIS score was calculated based on these five indicators.For overall survival prediction,the respective C-indexes in the training set were 0.915(95%confidence interval:0.866-0.964)for overall survival prediction and 0.908(95%confidence interval:0.872-0.944)for progression-free survival prediction.According to decision curve analysis,net benefit of the GATIS score was higher than that of a single factor.The time-dependent area under the receiver operating characteristic curve showed that the predictive power of the GATIS score was higher than that of the TNM stage and pathological grade at all time periods.CONCLUSION The GATIS score had a good predictive effect on the prognosis of patients with R-NENs,with efficacy superior to that of the World Health Organization grade and TNM stage.

Genetic pathways in cerebral palsy:a review of the implications for precision diagnosis and understanding disease mechanisms

Ce rebral palsy is a diagnostic term utilized to describe a group of permanent disorders affecting movement and posture.Patients with cerebral palsy are often only capable of limited activity,resulting from non-progressive disturbances in the fetal or neonatal brain.These disturbances severely impact the child’s daily life and impose a substantial economic burden on the family.Although cerebral palsy encompasses various brain injuries leading to similar clinical outcomes,the unde rstanding of its etiological pathways remains incomplete owing to its complexity and heterogeneity.This review aims to summarize the current knowledge on the genetic factors influencing cerebral palsy development.It is now widely acknowledged that genetic mutations and alterations play a pivotal role in cerebral palsy development,which can be further influenced by environmental fa ctors.Des pite continuous research endeavors,the underlying fa ctors contributing to cerebral palsy remain are still elusive.However,significant progress has been made in genetic research that has markedly enhanced our comprehension of the genetic factors underlying cerebral palsy development.Moreove r,these genetic factors have been categorized based on the identified gene mutations in patients through clinical genotyping,including thrombosis,angiogenesis,mitochondrial and oxidative phosphorylation function,neuronal migration,and cellular autophagy.Furthermore,exploring targeted genotypes holds potential for precision treatment.In conclusion,advancements in genetic research have substantially improved our understanding of the genetic causes underlying cerebral palsy.These breakthroughs have the potential to pave the way for new treatments and therapies,consequently shaping the future of cerebral palsy research and its clinical management.The investigation of cerebral palsy genetics holds the potential to significantly advance treatments and management strategies.By elucidating the underlying cellular mechanisms,we can develop to rgeted interventions to optimize outcomes.A continued collaboration between researchers and clinicians is imperative to comprehensively unravel the intricate genetic etiology of cerebral palsy.

Winter wheat yield improvement by genetic gain across different provinces in China

The replacement of winter wheat varieties has contributed significantly to yield improvement worldwide,with remarkable progress in China.Drawing on two sets of data,production yield from the National Bureau of Statistics of China and experimental yield from literature,this study aims to(1)illustrate the increasing patterns of production yield among different provinces from 1978 to 2018 in China,(2)explore the genetic gain in yield and yield relevant traits through the variety replacement based on experimental yield from 1937 to 2016 in China,and(3)compare the yield gap between experimental yield and production yield.The results show that both the production and experimental yields significantly increased along with the variety replacement.The national annual yield increase ratio for the production yield was 1.67%from 1978 to 2018,varying from 0.96%in Sichuan Province to 2.78%in Hebei Province;such ratio for the experimental yield was 1.13%from 1937 to 2016.The yield gap between experimental and production yields decreased from the 1970s to the 2010s.This study reveals significant increases in some yield components consequent to variety replacement,including thousand-grain weight,kernel number per spike,and grain number per square meter;however,no change is shown in spike number per square meter.The biomass and harvest index consistently and significantly increased,whereas the plant height decreased significantly.

Mixed neuroendocrine non-neuroendocrine neoplasms in gastroenteropancreatic tract

Mixed neuroendocrine non-neuroendocrine neoplasms(MiNENs)are a hetero-geneous group of malignant neoplasms that can settle in the gastroenteropan-creatic tract.They are composed of a neuroendocrine(NE)and a non-NE compo-nent in at least 30%of each tumour.The non-NE component can include different histological combinations of glandular,squamous,mucinous and sarcomatoid phenotypes,and one or both of the components can be low-or high grade malignant.Recent changes in the nomenclature of these neoplasms might lead to great deal of confusion,and the lack of specific clinical trials is the main reason why their management is difficult.The review aims to clarify the definition of MiNEN and analyze available evidence about their diagnosis and treatment options according to their location and extension through careful analysis of the available data.It would be important to reach a general consensus on their diagnosis in order to construct a classification that remains stable over time and facilitates the design of clinical trials that,due to their low incidence,will require long recruitment periods.

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.

Endoscopic ultrasonography-related diagnostic accuracy and clinical significance on small rectal neuroendocrine neoplasms

This research aimed to examine the diagnostic accuracy and clinical significance of endoscopic ultrasonography(EUS)in the context of small rectal neuroendocrine neoplasms(NENs).A total of 108 patients with rectal subepithelial lesions(SELs)with a diameter of<20 mm were included in the analysis.The diagnosis and depth assessment of EUS was compared to the histology findings.The prevalence of NENs in rectal SELs was 78.7%(85/108).The sensitivity of EUS in detecting rectal NENs was 98.9%(84/85),while the specificity was 52.2%(12/23).Overall,the diagnostic accuracy of EUS in identifying rectal NENs was 88.9%(96/108).The overall accuracy rate for EUS in assessing the depth of invasion in rectal NENs was 92.9%(78/84).Therefore,EUS demonstrates reasonable diagnostic accuracy in detecting small rectal NENs,with good sensitivity but inferior specificity.EUS may also assist physicians in assessing the depth of invasion in small rectal NENs before endoscopic excision.

Genetic variants in C1GALT1 are associated with gastric cancer risk by influencing immune infiltration

Core 1 synthase glycoprotein-N-acetylgalactosamine 3-β-galactosyltransferase 1(C1GALT1)is known to play a critical role in the development of gastric cancer,but few studies have elucidated associations between genetic variants in C1GALT1 and gastric cancer risk.By using the genome-wide association study data from the database of Genotype and Phenotype(dbGAP),we evaluated such associations with a multivariable logistic regression model and identified that the rs35999583 G>C in C1GALT1 was associated with gastric cancer risk(odds ratio,0.83;95% confidence interval[CI],0.75-0.92;P=3.95×10^(-4)).C1GALT1 mRNA expression levels were significantly higher in gastric tumor tissues than in normal tissues,and gastric cancer patients with higher C1GALT1 mRNA levels had worse overall survival rates(hazards ratio,1.33;95%CI,1.05-1.68;P_(log-rank)=1.90×10^(-2)).Furthermore,we found that C1GALT1 copy number differed in various immune cells and that C1GALT1 mRNA expression levels were positively correlated with the infiltrating levels of CD4^(+)T cells and macrophages.These results suggest that genetic variants of C1GALT1 may play an important role in gastric cancer risk and provide a new insight for C1GALT1 into a promising predictor of gastric cancer susceptibility and immune status.

Genetically modified pigs:Emerging animal models for hereditary hearing loss

Hereditary hearing loss(HHL),a genetic disorder that impairs auditory function,significantly affects quality of life and incurs substantial economic losses for society.To investigate the underlying causes of HHL and evaluate therapeutic outcomes,appropriate animal models are necessary.Pigs have been extensively used as valuable large animal models in biomedical research.In this review,we highlight the advantages of pig models in terms of ear anatomy,inner ear morphology,and electrophysiological characteristics,as well as recent advancements in the development of distinct genetically modified porcine models of hearing loss.Additionally,we discuss the prospects,challenges,and recommendations regarding the use pig models in HHL research.Overall,this review provides insights and perspectives for future studies on HHL using porcine models.

Identifying the Hydrochemical Characteristics,Genetic Mechanisms and Potential Human Health Risks of Fluoride and Nitrate Enriched Groundwater in the Tongzhou District,Beijing,North China

Fluoride and nitrate enriched groundwater are potential threats to the safety of the groundwater supply that may cause significant effects on human health and public safety,especially in aggregated population areas and economic hubs.This study focuses on the high F^(−)and NO_(3)^(−)concentration groundwater in Tongzhou District,Beijing,North China.A total of 36 groundwater samples were collected to analyze the hydrochemical characteristics,elucidate genetic mechanisms and evaluate the potential human health risks.The results of the analysis indicate:Firstly,most of the groundwater samples are characterized by Mg-HCO_(3) and Na-HCO_(3) with the pH ranging from 7.19 to 8.28 and TDS with a large variation across the range 471-2337 mg/L.The NO_(3)^(−)concentration in 38.89%groundwater samples and the F^(−)concentration in 66.67%groundwater samples exceed the permissible limited value.Secondly,F^(−)in groundwater originates predominantly from water-rock interactions and the fluorite dissolution,which is also regulated by cation exchange,competitive adsorption of HCO_(3)−and an alkaline environment.Thirdly,the effect of sewage disposal and agricultural activities have a significant effect on high NO3-concentration,while the high F^(−)concentration is less influenced by anthropogenic activity.The alkaline environment favors nitrification,thus being conducive to the production of NO_(3)^(−).Finally,the health risk assessment is evaluated for different population groups.The results indicate that high NO_(3)^(−)and F^(−)concentration in groundwater would have the largest threat to children’s health.The findings of this study could contribute to the provision of a scientific basis for groundwater supply policy formulation relating to public health in Tongzhou District.

Conservation genomic investigation of an endangered conifer,Thuja sutchuenensis,reveals low genetic diversity but also low genetic load

Endangered species generally have small populations with low genetic diversity and a high genetic load.Thuja sutchuenensis is an endangered conifer endemic to southwestern China.It was once considered extinct in the wild,but in 1999 was rediscovered.However,little is known about its genetic load.We collected 67 individuals from five wild,isolated T.sutchuenensis populations,and used 636,151 SNPs to analyze the level of genetic diversity and genetic load in T.sutchuenensis to delineate the conservation units of T.sutchuenensis,based on whole transcriptome sequencing data,as well as target capture sequencing data.We found that populations of T.sutchuenensis could be divided into three groups.These groups had low levels genetic diversity and were moderately genetically differentiated.Our findings also indicate that T.sutchuenensis suffered two severe bottlenecks around the Last Glaciation Period and Last Glacial Maximum.Among Thuja species,T.sutchuenensis presented the lowest genetic load and hence might have purged deleterious mutations efficiently through purifying selection.However,distribution of fitness effects analysis indicated a high extinction risk for T.sutchuenensis.Multiple lines of evidence identified three management units for T.sutchuenensis.Although T.sutchuenensis possesses a low genetic load,low genetic diversity,suboptimal fitness,and anthropogenic pressures all present an extinction risk for this rare conifer.This might also hold true for many endangered plant species in the mountains all over the world.

Inflammation as a cause of acute myocardial infarction in patients with myeloproliferative neoplasm

Myeloproliferative neoplasms(MPN)are a group of diseases characterized by the clonal proliferation of hematopoietic progenitor or stem cells.They are clinically classifiable into four main diseases:chronic myeloid leukemia,essential thrombocythemia,polycythemia vera,and primary myelofibrosis.These pathologies are closely related to cardio-and cerebrovascular diseases due to the increased risk of arterial thrombosis,the most common underlying cause of acute myocardial infarction.Recent evidence shows that the classical Virchow triad(hypercoagulability,blood stasis,endothelial injury)might offer an explanation for such association.Indeed,patients with MPN might have a higher number and more reactive circulating platelets and leukocytes,a tendency toward blood stasis because of a high number of circulating red blood cells,endothelial injury or overactivation as a consequence of sustained inflammation caused by the neoplastic clonal cell.These abnormal cancer cells,especially when associated with the JAK2V617F mutation,tend to proliferate and secrete several inflammatory cytokines.This sustains a pro-inflammatory state throughout the body.The direct consequence is the induction of a pro-thrombotic state that acts as a determinant in favoring both venous and arterial thrombus formation.Clinically,MPN patients need to be carefully evaluated to be treated not only with cytoreductive treatments but also with cardiovascular protective strategies.

Genetic variation of circHIBADH enhances prostate cancer risk through regulating HNRNPA1-related RNA splicing

The current study aimed to investigate associations of circRNAs and related genetic variants with the risk of prostate cancer(PCa)as well as to elucidate biological mechanisms underlying the associations.We first compared expression levels of circRNAs between 25 paired PCa and adjacent normal tissues to identify riskassociated circRNAs by using the MiOncoCirc database.We then used logistic regression models to evaluate associations between genetic variants in candidate circRNAs and PCa risk among 4662 prostate cancer patients and 3114 healthy controls,and identified circHIBADH rs11973492 T>C as a significant risk-associated variant(odds ratio=1.20,95%confidence interval:1.08-1.34,P=7.06×10^(-4))in a dominant genetic model,which altered the secondary structure of the corresponding RNA chain.In the in silico analysis,we found that circHIBADH sponged and silenced 21 RNA-binding proteins(RBPs)enriched in the RNA splicing pathway,among which HNRNPA1 was identified and validated as a hub RBP using an external RNA-sequencing data as well as the in-house(four tissue samples)and publicly available single-cell transcriptomes.Additionally,we demonstrated that HNRNPA1 influenced hallmarks including MYC target,DNA repair,and E2F target signaling pathways,thereby promoting carcinogenesis.In conclusion,genetic variants in circHIBADH may act as sponges and inhibitors of RNA splicing-associated RBPs including HNRNPA1,playing an oncogenic role in PCa.