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2.
Children (Basel) ; 11(9)2024 Aug 30.
Article in English | MEDLINE | ID: mdl-39334598

ABSTRACT

BACKGROUND: Childhood blindness remains a neglected issue in eye care within low-income countries, with congenital and juvenile cataracts being the most common treatable causes. This study aims to investigate the factors influencing the management of congenital and juvenile bilateral cataracts, provide data on general outcomes and postoperative findings, and discuss treatment in a low-income country context. METHODS: In this prospective study, data from clinical care were continuously entered into a database, and one follow-up examination of a cohort of 91 patients with congenital and juvenile bilateral cataracts in Kinshasa, Democratic Republic of the Congo, was conducted. Multiple factors that affect the first clinical presentation, the clinical management, and outcome were investigated. RESULTS: Most patients (88.5%) who received medical treatment were identified by cataract finders. A patient's presentation time was independent of the parent's education, social status, income, and sex of the child. The median age at first presentation was 5.8 years (ranging from 0 days to 17.3 years). The best visual acuity outcomes were achieved by patients who underwent surgery during early childhood. According to WHO grades and on an eye level basis, 51.1% (93 out of 182 eyes) showed improvement, while 34.6% (63 eyes) had unchanged results post-surgery. Among the cases without improvement, 76.2% were blind prior to surgery. Postoperative findings were observed in 56% of the patients, with secondary cataracts being the most common, affecting 26.37% of the operated eyes. CONCLUSIONS: Optimal management of childhood cataracts involves early identification, efficient hospital infrastructure, high-quality medical care, and long-term follow up. In sub-Saharan Africa, this approach must be adapted to the context of available resources, which differs significantly from those in high- and middle-income countries.

3.
Ophthalmol Sci ; 4(6): 100565, 2024.
Article in English | MEDLINE | ID: mdl-39253548

ABSTRACT

Purpose: To evaluate the performance of a disease activity (DA) model developed to detect DA in participants with neovascular age-related macular degeneration (nAMD). Design: Post hoc analysis. Participants: Patient dataset from the phase III HAWK and HARRIER (H&H) studies. Methods: An artificial intelligence (AI)-based DA model was developed to generate a DA score based on measurements of OCT images and other parameters collected from H&H study participants. Disease activity assessments were classified into 3 categories based on the extent of agreement between the DA model's scores and the H&H investigators' decisions: agreement ("easy"), disagreement ("noisy"), and close to the decision boundary ("difficult"). Then, a panel of 10 international retina specialists ("panelists") reviewed a sample of DA assessments of these 3 categories that contributed to the training of the final DA model. A panelists' majority vote on the reviewed cases was used to evaluate the accuracy, sensitivity, and specificity of the DA model. Main Outcome Measures: The DA model's performance in detecting DA compared with the DA assessments made by the investigators and panelists' majority vote. Results: A total of 4472 OCT DA assessments were used to develop the model; of these, panelists reviewed 425, categorized as "easy" (17.2%), "noisy" (20.5%), and "difficult" (62.4%). False-positive and false negative rates of the DA model's assessments decreased after changing the assessment in some cases reviewed by the panelists and retraining the DA model. Overall, the DA model achieved 80% accuracy. For "easy" cases, the DA model reached 96% accuracy and performed as well as the investigators (96% accuracy) and panelists (90% accuracy). For "noisy" cases, the DA model performed similarly to panelists and outperformed the investigators (84%, 86%, and 16% accuracies, respectively). The DA model also outperformed the investigators for "difficult" cases (74% and 53% accuracies, respectively) but underperformed the panelists (86% accuracy) owing to lower specificity. Subretinal and intraretinal fluids were the main clinical parameters driving the DA assessments made by the panelists. Conclusions: These results demonstrate the potential of using an AI-based DA model to optimize treatment decisions in the clinical setting and in detecting and monitoring DA in patients with nAMD. Financial Disclosures: Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

4.
Nat Commun ; 15(1): 7991, 2024 Sep 12.
Article in English | MEDLINE | ID: mdl-39266553

ABSTRACT

Interactions between adipose tissue, liver and immune system are at the center of metabolic dysfunction-associated steatotic liver disease and type 2 diabetes. To address the need for an accurate in vitro model, we establish an interconnected microphysiological system (MPS) containing white adipocytes, hepatocytes and proinflammatory macrophages derived from isogenic human induced pluripotent stem cells. Using this MPS, we find that increasing the adipocyte-to-hepatocyte ratio moderately affects hepatocyte function, whereas macrophage-induced adipocyte inflammation causes lipid accumulation in hepatocytes and MPS-wide insulin resistance, corresponding to initiation of metabolic dysfunction-associated steatotic liver disease. We also use our MPS to identify and characterize pharmacological intervention strategies for hepatic steatosis and systemic insulin resistance and find that the glucagon-like peptide-1 receptor agonist semaglutide improves hepatocyte function by acting specifically on adipocytes. These results establish our MPS modeling the adipose tissue-liver axis as an alternative to animal models for mechanistic studies or drug discovery in metabolic diseases.


Subject(s)
Hepatocytes , Induced Pluripotent Stem Cells , Inflammation , Insulin Resistance , Liver , Humans , Induced Pluripotent Stem Cells/metabolism , Hepatocytes/metabolism , Hepatocytes/drug effects , Liver/metabolism , Liver/pathology , Inflammation/metabolism , Inflammation/pathology , Adipocytes/metabolism , Macrophages/metabolism , Macrophages/drug effects , Fatty Liver/metabolism , Fatty Liver/pathology , Glucagon-Like Peptide-1 Receptor/metabolism , Glucagon-Like Peptide-1 Receptor/agonists , Glucagon-Like Peptide-1 Receptor/genetics , Adipose Tissue/metabolism , Microphysiological Systems
5.
BMC Plant Biol ; 24(1): 856, 2024 Sep 13.
Article in English | MEDLINE | ID: mdl-39266950

ABSTRACT

BACKGROUND: The frequency and severity of abiotic stress events, especially drought, are increasing due to climate change. The plant root is the most important organ for water uptake and the first to be affected by water limitation. It is therefore becoming increasingly important to include root traits in studies on drought stress tolerance. However, phenotyping under field conditions remains a challenging task. In this study, plants were grown in a hydroponic system with polyethylene glycol as an osmotic stressor and in sand pots to examine the root system of eleven spring barley genotypes. The root anatomy of two genotypes with different response to drought was investigated microscopically. RESULTS: Root diameter increased significantly (p < 0.05) under polyethylene glycol treatment by 54% but decreased significantly (p < 0.05) by 12% under drought stress in sand pots. Polyethylene glycol treatment increased root tip diameter (51%) and reduced diameter of the elongation zone (14%) compared to the control. Under drought stress, shoot mass of plants grown in sand pots showed a higher correlation (r = 0.30) with the shoot mass under field condition than polyethylene glycol treated plants (r = -0.22). CONCLUSION: These results indicate that barley roots take up polyethylene glycol by the root tip and polyethylene glycol prevents further water uptake. Polyethylene glycol-triggered osmotic stress is therefore unsuitable for investigating root morphology traits in barley. Root architecture of roots grown in sand pots is more comparable to roots grown under field conditions.


Subject(s)
Hordeum , Plant Roots , Polyethylene Glycols , Hordeum/drug effects , Hordeum/anatomy & histology , Hordeum/growth & development , Hordeum/physiology , Hordeum/genetics , Plant Roots/anatomy & histology , Plant Roots/drug effects , Plant Roots/growth & development , Polyethylene Glycols/pharmacology , Droughts , Genotype , Stress, Physiological
6.
Nat Commun ; 15(1): 7522, 2024 Aug 30.
Article in English | MEDLINE | ID: mdl-39215042

ABSTRACT

Activated Wnt/ß-catenin pathway is a key genetic event in liver cancer development. Solute carrier (SLC) transporters are promising drug targets. Here, we identify SLC13A3 as a drug-targetable effector downstream of ß-catenin in liver cancer. SLC13A3 expression is elevated in human liver cancer samples with gain of function (GOF) mutant CTNNB1, the gene encoding ß-catenin. Activation of ß-catenin up-regulates SLC13A3, leading to intracellular accumulation of endogenous SLC13A3 substrates. SLC13A3 is identified as a low-affinity transporter for glutathione (GSH). Silencing of SLC13A3 downregulates the leucine transporter SLC7A5 via c-MYC signaling, leading to leucine depletion and mTOR inactivation. Furthermore, silencing of SLC13A3 depletes GSH and induces autophagic ferroptosis in ß-catenin-activated liver cancer cells. Importantly, both genetic inhibition of SLC13A3 and a small molecule SLC13A3 inhibitor suppress ß-catenin-driven hepatocarcinogenesis in mice. Altogether, our study suggests that SLC13A3 could be a promising therapeutic target for treating human liver cancers with GOF CTNNB1 mutations.


Subject(s)
Liver Neoplasms , beta Catenin , Animals , Humans , Male , Mice , Amino Acid Transport System y+/metabolism , Amino Acid Transport System y+/genetics , beta Catenin/metabolism , beta Catenin/genetics , Carcinoma, Hepatocellular/metabolism , Carcinoma, Hepatocellular/genetics , Carcinoma, Hepatocellular/pathology , Cell Line, Tumor , Gene Expression Regulation, Neoplastic , Glutathione/metabolism , Large Neutral Amino Acid-Transporter 1 , Leucine/metabolism , Liver Neoplasms/metabolism , Liver Neoplasms/genetics , Liver Neoplasms/pathology , Proto-Oncogene Proteins c-myc/metabolism , Proto-Oncogene Proteins c-myc/genetics , TOR Serine-Threonine Kinases/metabolism , Wnt Signaling Pathway
7.
JAMA Netw Open ; 7(7): e2423933, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-39052290

ABSTRACT

Importance: Retinopathy of prematurity (ROP) is a major morbidity of preterm infants causing visual impairment, including blindness, for which timely treatment is vital and prevention is key. Increasing evidence suggests that exposure to neonatal sepsis contributes to ROP development. Objective: To investigate the association between neonatal sepsis and ROP in 2 large-scale cohorts of preterm infants born at less than 29 weeks' gestation. Design, Setting, and Participants: This retrospective cohort study was conducted using data from the German Neonatal Network (GNN) and Norwegian Neonatal Network (NNN). The GNN involves 68 and the NNN includes 21 level III neonatal intensive care units. Participants were infants born at a gestation of 22 weeks and 0 days to 28 weeks and 6 days and enrolled in the GNN between January 1, 2009, and December 31, 2022, and NNN between January 1, 2009, and December 31, 2018. Data were analyzed from February through September 2023. Exposure: Single or multiple episodes of culture-proven sepsis. Main Outcomes and Measures: Any ROP and treatment-warranted ROP. Results: Among 12 794 infants in the GNN (6043 female [47.2%] and 6751 male [52.8%]; mean [SD] gestational age, 26.4 [1.5] weeks) and 1844 infants in the NNN (866 female [47.0%] and 978 male [53.0%]; mean [SD] gestational age, 25.6 [1.5] weeks), the mean (SD) birth weight was 848 (229) g and 807 (215) g, respectively. Any ROP was present in 6370 infants (49.8%) in GNN and 620 infants (33.6%) in NNN, and treatment-warranted ROP was present in 840 infants (6.6%) in GNN and 140 infants (7.6%) in NNN. In both cohorts, there were increasing rates of treatment-warranted ROP with each sepsis episode (no sepsis: 572 of 10 658 infants [5.4%] in GNN and 85 of 1492 infants (5.7%) in NNN; 1 episode: 190 of 1738 infants in GNN [10.9%] and 29 of 293 infants [9.9%] in NNN; 2 episodes: 53 of 314 infants in GNN [16.9%] and 13 of 49 infants [26.5%] in NNN; 3 episodes: 25 of 84 infants [29.8%] in GNN and 3 of 10 infants [30.0%] in NNN). After adjusting for multiple confounders in the GNN dataset, the number of sepsis episodes was associated with ROP and treatment-warranted ROP compared with 0 episodes (1 episode: adjusted odds ratio [aOR], 1.44 [95% CI, 1.27-1.63]; P < .001 and OR, 1.60 [95% CI, 1.31-1.96]; P < .001, respectively; 2 episodes: OR, 1.81 [95% CI, 1.35-2.42]; P < .001 and OR, 2.38 [95% CI, 1.68-3.37]; P < .001, respectively; 3 episodes: OR, 4.39 [95% CI, 2.19-8.78]; P < .001 and OR, 3.88 [95% CI, 2.29-6.55]; P < .001, respectively). These associations were confirmed for any ROP by propensity score matching (for example, the aOR with propensity score matching was 1.76 [95% CI, 1.54-2.02]; P < .001 for 1 episode vs 0 episodes and 1.58 [95% CI, 1.12-2.22]; P = .007 for 3 episodes vs 0 or 1 episode). In the NNN dataset, surgical NEC was associated with treatment-warranted ROP (multivariable analysis: aOR, 3.37 [95% CI, 1.78-6.37]; P < .001). Conclusions and Relevance: This study found that in the large-scale GNN cohort, recurrent culture-proven sepsis was associated with ROP and treatment-warranted ROP in infants born at less than 29 weeks.


Subject(s)
Neonatal Sepsis , Retinopathy of Prematurity , Humans , Retinopathy of Prematurity/epidemiology , Infant, Newborn , Female , Male , Retrospective Studies , Neonatal Sepsis/epidemiology , Germany/epidemiology , Infant, Extremely Premature , Norway/epidemiology , Intensive Care Units, Neonatal/statistics & numerical data , Gestational Age , Infant, Premature , Risk Factors
8.
Plant Phenomics ; 6: 0215, 2024.
Article in English | MEDLINE | ID: mdl-39049840

ABSTRACT

Phenomic selection is a recent approach suggested as a low-cost, high-throughput alternative to genomic selection. Instead of using genetic markers, it employs spectral data to predict complex traits using equivalent statistical models. Phenomic selection has been shown to outperform genomic selection when using spectral data that was obtained within the same generation as the traits that were predicted. However, for hybrid breeding, the key question is whether spectral data from parental genotypes can be used to effectively predict traits in the hybrid generation. Here, we aimed to evaluate the potential of phenomic selection for hybrid rapeseed breeding. We performed predictions for various traits in a structured population of 410 test hybrids, grown in multiple environments, using near-infrared spectroscopy data obtained from harvested seeds of both the hybrids and their parental lines with different linear and nonlinear models. We found that phenomic selection within the hybrid generation outperformed genomic selection for seed yield and plant height, even when spectral data was collected at single locations, while being less affected by population structure. Furthermore, we demonstrate that phenomic prediction across generations is feasible, and selecting hybrids based on spectral data obtained from parental genotypes is competitive with genomic selection. We conclude that phenomic selection is a promising approach for rapeseed breeding that can be easily implemented without any additional costs or efforts as near-infrared spectroscopy is routinely assessed in rapeseed breeding.

9.
Physiol Plant ; 176(3): e14315, 2024.
Article in English | MEDLINE | ID: mdl-38693794

ABSTRACT

Rapeseed (Brassica napus L.) is an oil-containing crop of great economic value but with considerable nitrogen requirement. Breeding root systems that efficiently absorb nitrogen from the soil could be a driver to ensure genetic gains for more sustainable rapeseed production. The aim of this study is to identify genomic regions that regulate root morphology in response to nitrate availability. The natural variability offered by 300 inbred lines was screened at two experimental locations. Seedlings grew hydroponically with low or elevated nitrate levels. Fifteen traits related to biomass production and root morphology were measured. On average across the panel, a low nitrate level increased the root-to-shoot biomass ratio and the lateral root length. A large phenotypic variation was observed, along with important heritability values and genotypic effects, but low genotype-by-nitrogen interactions. Genome-wide association study and bulk segregant analysis were used to identify loci regulating phenotypic traits. The first approach nominated 319 SNPs that were combined into 80 QTLs. Three QTLs identified on the A07 and C07 chromosomes were stable across nitrate levels and/or experimental locations. The second approach involved genotyping two groups of individuals from an experimental F2 population created by crossing two accessions with contrasting lateral root lengths. These individuals were found in the tails of the phenotypic distribution. Co-localized QTLs found in both mapping approaches covered a chromosomal region on the A06 chromosome. The QTL regions contained some genes putatively involved in root organogenesis and represent selection targets for redesigning the root morphology of rapeseed.


Subject(s)
Brassica napus , Nitrogen , Phenotype , Plant Roots , Quantitative Trait Loci , Plant Roots/genetics , Plant Roots/anatomy & histology , Plant Roots/growth & development , Plant Roots/metabolism , Nitrogen/metabolism , Quantitative Trait Loci/genetics , Brassica napus/genetics , Brassica napus/growth & development , Brassica napus/anatomy & histology , Brassica napus/metabolism , Genotype , Genome-Wide Association Study , Polymorphism, Single Nucleotide/genetics , Biomass , Nitrates/metabolism , Chromosome Mapping , Genetic Variation
10.
Med Sci Monit ; 30: e943140, 2024 May 04.
Article in English | MEDLINE | ID: mdl-38702879

ABSTRACT

BACKGROUND Age-related macular degeneration (AMD) is the most common cause of visual impairment in the elderly population in industrialized countries. The Study of Health in Pomerania (SHIP) with its cohort SHIP-TREND was designed to investigate risk factors and clinical disorders in the general population of northeast Germany. This work focused on the first follow-up of SHIP-TREND and determined associated modifiable risk factors of AMD. Modifying risk factors is important to slow the progression of early AMD as there is currently no treatment for the late stage of geographic atrophy. Understanding AMD-associated risk factors also plays an important role in the development of therapeutic concepts. MATERIAL AND METHODS Between 2016 and 2019, data were collected from a total of 2507 initially randomly selected subjects from the general population aged 28 to 89 years. Non-mydriatic fundus photography of the right eye was performed in 2489 subjects. Grading of AMD was performed using the Rotterdam classification system. RESULTS We included 1418 gradable fundus photographs in the analysis. The risk of AMD changes increased with age and was positively correlated with HDL cholesterol, fT3, and low educational level. In men, BMI and cigarette smoking were also positively associated with AMD changes. CONCLUSIONS This study emphasizes the consideration of various metabolic pathways for the development of therapeutic concepts.


Subject(s)
Macular Degeneration , Humans , Macular Degeneration/epidemiology , Male , Aged , Risk Factors , Female , Germany/epidemiology , Middle Aged , Aged, 80 and over , Adult , Cohort Studies
11.
Theor Appl Genet ; 137(6): 125, 2024 May 10.
Article in English | MEDLINE | ID: mdl-38727862

ABSTRACT

KEY MESSAGE: PHOTOPERIOD-1 homoeologous gene copies play a pivotal role in regulation of flowering time in wheat. Here, we show that their influence also extends to spike and shoot architecture and even impacts root development. The sequence diversity of three homoeologous copies of the PHOTOPERIOD-1 gene in European winter wheat was analyzed by Oxford Nanopore amplicon-based multiplex sequencing and molecular markers in a panel of 194 cultivars representing breeding progress over the past 5 decades. A strong, consistent association with an average 8% increase in grain yield was observed for the PpdA1-Hap1 haplotype across multiple environments. This haplotype was found to be linked in 51% of cultivars to the 2NS/2AS translocation, originally introduced from Aegilops ventricosa, which leads to an overestimation of its effect. However, even in cultivars without the 2NS/2AS translocation, PpdA1-Hap1 was significantly associated with increased grain yield, kernel per spike and kernel per m2 under optimal growth conditions, conferring a 4% yield advantage compared to haplotype PpdA1-Hap4. In contrast to Ppd-B1 and Ppd-D1, the Ppd-A1 gene exhibits novel structural variations and a high number of SNPs, highlighting the evolutionary changes that have occurred in this region over the course of wheat breeding history. Additionally, cultivars carrying the photoperiod-insensitive Ppd-D1a allele not only exhibit earlier heading, but also deeper roots compared to those with photoperiod-sensitive alleles under German conditions. PCR and KASP assays have been developed that can be effectively employed in marker-assisted breeding programs to introduce these favorable haplotypes.


Subject(s)
Haplotypes , Plant Roots , Triticum , Triticum/genetics , Triticum/growth & development , Plant Roots/genetics , Plant Roots/growth & development , Phenotype , Polymorphism, Single Nucleotide , Plant Breeding , Photoperiod , Genes, Plant , Genetic Markers
12.
Ophthalmology ; 2024 May 23.
Article in English | MEDLINE | ID: mdl-38795976

ABSTRACT

PURPOSE: The International Classification of Retinopathy of Prematurity, Third Edition (ICROP3), acknowledged that plus-like retinopathy of prematurity (ROP) vascular changes occurs along a spectrum. Historically, clinician-experts demonstrate variable agreement for plus diagnosis. We developed a 9-photograph reference image set for grading plus-like changes and compared intergrader agreement of the set with standard grading with no plus, preplus, and plus disease. DESIGN: Retinal photographic grading and expert consensus opinion. PARTICIPANTS: The development set included 34 international ICROP3 committee members. The validation set included 30 ophthalmologists with ROP expertise (15 ICROP3 committee members and 15 non-ICROP3 members) METHODS: Nine ROP fundus images (P1 through P9) representing increasing degrees of zone I vascular tortuosity and dilation, based on the 34 ICROP3 committee members' gradings and consensus image reviews, were used to establish standard photographs for the plus (P) score. Study participants graded 150 fundus photographs 2 ways, separated by a 1-week washout period: (1) no plus, preplus, or plus disease and (2) choosing the closest P score image. MAIN OUTCOME MEASURES: Intergrader agreement measured by intraclass correlation coefficient. RESULTS: Intergrader agreement was higher using the P score (intraclass correlation coefficient, 0.75; 95% confidence interval, 0.71-0.79) than no plus, preplus, or plus disease (intraclass correlation coefficient, 0.67; 95% confidence interval, 0.62-0.72). Mean ± standard deviation P scores for images with mode gradings of no plus, preplus, and plus disease were 2.5 ± 0.7, 4.8 ± 0.8, and 7.4 ± 0.8, respectively. CONCLUSIONS: Intergrader agreement of plus-like vascular change in ROP using the P score is high. We now incorporate this 9-image reference set into ICROP3 for use in clinician daily practice alongside zone, stage, and plus assessment. P score is not yet meant to replace plus diagnosis for treatment decisions, but its use at our institutions has permitted better comparison between examinations for progression and regression, communication between examiners, and documentation of vascular change without fundus imaging. P score also could provide more detailed ROP classification for clinical trials, consistent with the spectrum of plus-like change that is now formally part of the International Classification of Retinopathy of Prematurity. FINANCIAL DISCLOSURE(S): Proprietary or commercial disclosure may be found in the Footnotes and Disclosures at the end of this article.

13.
Article in English | MEDLINE | ID: mdl-38816192

ABSTRACT

OBJECTIVE: Retinopathy of prematurity (ROP) is a leading yet avoidable cause of childhood blindness. Screening for ROP is highly effective in preventing blindness secondary to ROP. We provide epidemiological data on ROP screening and treatment in Germany since 2010 and evaluate the effects of recently adopted as well as potential future screening guideline adaptations. METHODS: Data sets of the German Quality Assurance Procedure in Neonatology, the ROP screening programme of two German university hospitals, and the German section of the EU-ROP Registry were analysed. RESULTS: Over the 13-year period from 2010 to 2022, 141 550 infants received ROP screening in Germany. Mean annual incidences of ROP were 3.5% (±0.2%) in premature infants and 19.6% (±2.3%) in screened infants. Of screened infants, 2.0% (±0.3%) received treatment for ROP. Treatment preferences shifted from laser coagulation (46.2% in 2015) to anti-vascular endothelial growth factor therapy (83.7% in 2022). A revision of national screening criteria in 2020 with a reduction of the gestational age limit from <32 to <31 weeks resulted in a decrease of the annual number of infants requiring screening by 25.8% (p<0.001). Infants with a birth weight ≥1500 g accounted for 35.2% of the screening population but only for 0.4% of ROP stage 3-5 cases. CONCLUSIONS: Collection of epidemiological data on ROP in national and international registries enables the continuous surveillance and adaptation of ROP screening and treatment criteria. In Germany, infants with a birth weight ≥1500 g have a very low risk of developing treatment-requiring ROP, supporting an upper birth weight limit for ROP screening.

14.
Genome ; 67(7): 210-222, 2024 Jul 01.
Article in English | MEDLINE | ID: mdl-38708850

ABSTRACT

Advances in sequencing technology allow whole plant genomes to be sequenced with high quality. Combining genotypic and phenotypic data in genomic prediction helps breeders to select crossing partners in partially phenotyped populations. In plant breeding programs, the cost of sequencing entire breeding populations still exceeds available genotyping budgets. Hence, the method for genotyping is still mainly single nucleotide polymorphism (SNP) arrays; however, arrays are unable to assess the entire genome- and population-wide diversity. A compromise involves genotyping the entire population using an SNP array and a subset of the population with whole-genome sequencing. Both datasets can then be used to impute markers from whole-genome sequencing onto the entire population. Here, we evaluate whether imputation of whole-genome sequencing data enhances genomic predictions, using data from a nested association mapping population of rapeseed (Brassica napus). Employing two cross-validation schemes that mimic scenarios for the prediction of close and distant relatives, we show that imputed marker data do not significantly improve prediction accuracy, likely due to redundancy in relationship estimates and imputation errors. In simulation studies, only small improvements were observed, further corroborating the findings. We conclude that SNP arrays are already equipped with the information that is added by imputation through relationship and linkage disequilibrium.


Subject(s)
Brassica napus , Genome, Plant , Polymorphism, Single Nucleotide , Whole Genome Sequencing , Brassica napus/genetics , Whole Genome Sequencing/methods , Plant Breeding/methods , Linkage Disequilibrium , Genomics/methods , Genotype
15.
EClinicalMedicine ; 71: 102567, 2024 May.
Article in English | MEDLINE | ID: mdl-38638400

ABSTRACT

Background: Concerns remain over the long-term safety of vascular endothelial growth factor (VEGF) inhibitors to treat retinopathy of prematurity (ROP). RAINBOW is an open label randomised trial comparing intravitreal ranibizumab (in 0.2 mg and 0.1 mg doses) with laser therapy in very low birthweight infants (<1500 g) with ROP. Methods: Of 201 infants completing RAINBOW, 180 were enrolled in the RAINBOW Extension Study. At 5 years, children underwent ophthalmic, development and health assessments. The primary outcome was visual acuity in the better-seeing eye. The study is registered with ClinicalTrial.gov, NCT02640664. Findings: Between 16-6-2016 and 21-4-2022, 156 children (87%) were evaluated at 5 years. Of 32 children with no acuity test result, 25 had a preferential looking test, for 4 children investigators reported low vision for each eye, and in 3 further children no vision measurement was obtained. 124 children completed the acuity assessment, the least square mean (95% CI) letter score in the better seeing eye was similar in the three trial arms-66.8 (62.9-70.7) following ranibizumab 0.2 mg, 64.6 (60.6-68.5) following ranibizumab 0.1 mg and 62.1 (57.8-66.4) following laser therapy; differences in means: ranibizumab 0.2 mg v laser: 4.7 (95% CI: -1.1, 10.5); 0.1 mg v laser: 2.5 (-3.4, 8.3); 0.2 mg v 0.1 mg: 2.2 (-3.3, 7.8). High myopia (worse than -5 dioptres) in at least one eye occurred in 4/52 (8%) children following ranibizumab 0.2 mg, 8/55 (15%) following ranibizumab 0.1 mg and 11/45 (24%) following laser therapy (0.2 mg versus laser: odds ratio: 3.99 (1.16-13.72)). Ocular and systemic secondary outcomes and adverse events were distributed similarly in each trial arm. Interpretation: 5-year outcomes confirm the findings of the original RAINBOW trial and a planned interim analysis at 2 years, including a reduced frequency of high myopia following ranibizumab treatment. No effects of treatment on non-ocular outcomes were detected. Funding: Novartis Pharma AG.

16.
bioRxiv ; 2024 Apr 06.
Article in English | MEDLINE | ID: mdl-38617333

ABSTRACT

Hyaluronic acid (HA), the primary component of brain extracellular matrix, is increasingly used to model neuropathological processes, including glioblastoma (GBM) tumor invasion. While elastic hydrogels based on crosslinked low-molecular-weight (LMW) HA are widely exploited for this purpose and have proven valuable for discovery and screening, brain tissue is both viscoelastic and rich in high-MW (HMW) HA, and it remains unclear how these differences influence invasion. To address this question, hydrogels comprised of either HMW (1.5 MDa) or LMW (60 kDa) HA are introduced, characterized, and applied in GBM invasion studies. Unlike LMW HA hydrogels, HMW HA hydrogels relax stresses quickly, to a similar extent as brain tissue, and to a greater extent than many conventional HA-based scaffolds. GBM cells implanted within HMW HA hydrogels invade much more rapidly than in their LMW HA counterparts and exhibit distinct leader-follower dynamics. Leader cells adopt dendritic morphologies, similar to invasive GBM cells observed in vivo. Transcriptomic, pharmacologic, and imaging studies suggest that leader cells exploit hyaluronidase, an enzyme strongly enriched in human GBMs, to prime a path for followers. This study offers new insight into how HA viscoelastic properties drive invasion and argues for the use of highly stress-relaxing materials to model GBM.

17.
JAMA Netw Open ; 7(4): e248383, 2024 Apr 01.
Article in English | MEDLINE | ID: mdl-38687481

ABSTRACT

Importance: Prospective long-term data after retinopathy of prematurity (ROP) treatment with anti-vascular endothelial growth factor injections vs laser therapy are scarce. The FIREFLEYE (Aflibercept for ROP IVT Injection vs Laser Therapy) next trial is prospectively evaluating the long-term efficacy and safety outcomes following ROP treatment with intravitreal aflibercept vs laser therapy. Objective: To evaluate 2-year ophthalmic and safety outcomes after 0.4-mg aflibercept injection or laser therapy in the 24-week randomized (2:1) FIREFLEYE trial (FIREFLEYE outcomes previously reported). Design, Setting, and Participants: This prospective nonrandomized controlled trial performed in 24 countries in Asia, Europe, and South America (2020-2025) follows up participants treated in the FIREFLEYE randomized clinical trial (2019-2021) through 5 years of age. Participants included children born very or extremely preterm (gestational age ≤32 weeks) or with very or extremely low birth weight (≤1500 g) who were previously treated with a 0.4-mg injection of aflibercept compared with laser therapy for severe acute-phase ROP. Data for the present interim analysis were acquired from March 18, 2020, to July 25, 2022. Interventions: Complications of ROP treated at investigator discretion (no study treatment). Main Outcomes and Measures: Efficacy end points included ROP status, unfavorable structural outcomes, ROP recurrence, treatment for ROP complications, completion of vascularization, and visual function. Safety end points included adverse events and growth and neurodevelopmental outcomes. Results: Overall, 100 children were enrolled (median gestational age, 26 [range, 23-31] weeks; 53 boys and 47 girls). Of these, 21 were Asian, 2 were Black, 75 were White, and 2 were of more than 1 race. At 2 years of age, 61 of 63 children (96.8%) in the aflibercept group vs 30 of 32 (93.8%) in the laser group had no ROP. Through 2 years of age, 62 of 66 (93.9%) in the aflibercept group and 32 of 34 (94.1%) in the laser group had no unfavorable structural outcomes. No new retinal detachment occurred during the study. Four children in the aflibercept group (6.1%) were treated for ROP complications before 1 year of age (2 had preexisting end-stage disease and total retinal detachment; 1 had reactivated plus disease; and 1 had recurrent retinal neovascularization not further specified). Most children were able to fix and follow a 5-cm toy (aflibercept group, 118 of 122 eyes [96.7%] among 63 children; laser group, 62 of 63 eyes [98.4%] among 33 children). High myopia was present in 9 of 115 eyes (7.8%) among 5 children in the aflibercept group and 13 of 60 eyes (21.7%) among 9 children in the laser group. No relevant differences in growth and neurodevelopmental outcomes by Bayley Scales of Infant and Toddler Development, Third Edition and Vineland Adaptive Behavior Scales, Second Edition were identified. Conclusions and Relevance: In this nonrandomized follow-up of a randomized clinical trial comparing treatment of severe acute-phase ROP with 0.4-mg injection of aflibercept and laser, disease control was stable and visual function was appropriate in children through 2 years of age. No adverse effects on safety, including growth and neurodevelopment, were identified. These findings provide clinically relevant long-term information on intravitreal aflibercept injection therapy for ROP. Trial Registration: ClinicalTrials.gov Identifier: NCT04015180.


Subject(s)
Angiogenesis Inhibitors , Intravitreal Injections , Receptors, Vascular Endothelial Growth Factor , Recombinant Fusion Proteins , Retinopathy of Prematurity , Humans , Retinopathy of Prematurity/surgery , Retinopathy of Prematurity/therapy , Retinopathy of Prematurity/drug therapy , Receptors, Vascular Endothelial Growth Factor/therapeutic use , Recombinant Fusion Proteins/therapeutic use , Recombinant Fusion Proteins/adverse effects , Recombinant Fusion Proteins/administration & dosage , Female , Male , Infant, Newborn , Prospective Studies , Treatment Outcome , Angiogenesis Inhibitors/therapeutic use , Angiogenesis Inhibitors/adverse effects , Laser Therapy/methods , Laser Therapy/adverse effects , Infant , Child, Preschool
18.
Mol Ther ; 32(5): 1425-1444, 2024 May 01.
Article in English | MEDLINE | ID: mdl-38504518

ABSTRACT

Pathological ocular angiogenesis has long been associated with myeloid cell activation. However, the precise cellular and molecular mechanisms governing the intricate crosstalk between the immune system and vascular changes during ocular neovascularization formation remain elusive. In this study, we demonstrated that the absence of the suppressor of cytokine signaling 3 (SOCS3) in myeloid cells led to a substantial accumulation of microglia and macrophage subsets during the neovascularization process. Our single-cell RNA sequencing data analysis revealed a remarkable increase in the expression of the secreted phosphoprotein 1 (Spp1) gene within these microglia and macrophages, identifying subsets of Spp1-expressing microglia and macrophages during neovascularization formation in angiogenesis mouse models. Notably, the number of Spp1-expressing microglia and macrophages exhibited further elevation during neovascularization in mice lacking myeloid SOCS3. Moreover, our investigation unveiled the Spp1 gene as a direct transcriptional target gene of signal transducer and activator of transcription 3. Importantly, pharmaceutical activation of SOCS3 or blocking of SPP1 resulted in a significant reduction in pathological neovascularization. In conclusion, our study highlights the pivotal role of the SOCS3/STAT3/SPP1 axis in the regulation of pathological retinal angiogenesis.


Subject(s)
Macrophages , Microglia , Osteopontin , Retinal Neovascularization , Suppressor of Cytokine Signaling 3 Protein , Animals , Mice , Angiogenesis , Disease Models, Animal , Gene Expression Regulation , Macrophages/metabolism , Mice, Knockout , Microglia/metabolism , Neovascularization, Pathologic/metabolism , Neovascularization, Pathologic/genetics , Osteopontin/metabolism , Osteopontin/genetics , Retinal Neovascularization/metabolism , Retinal Neovascularization/pathology , Retinal Neovascularization/genetics , Retinal Neovascularization/etiology , Signal Transduction , STAT3 Transcription Factor/metabolism , STAT3 Transcription Factor/genetics , Suppressor of Cytokine Signaling 3 Protein/metabolism , Suppressor of Cytokine Signaling 3 Protein/genetics
20.
BMC Plant Biol ; 24(1): 83, 2024 Feb 02.
Article in English | MEDLINE | ID: mdl-38308236

ABSTRACT

BACKGROUND: A sufficient nitrogen supply is crucial for high-quality wheat yields. However, the use of nitrogen fertilization can also negatively influence ecosystems due to leaching or volatile atmospheric emissions. Drought events, increasingly prevalent in many crop production areas, significantly impact nitrogen uptake. Breeding more efficient wheat varieties is necessary to achieve acceptable yields with limited nitrogen and water. Crop root systems play a crucial role as the primary organ for absorbing water and nutrients. To investigate the impact of an enhanced root system on nitrogen and water use efficiency in wheat under various irrigation conditions, this study conducted two experiments using precision phenotyping platforms for controlled drought stress treatment. Experiment 1 involved four contrasting winter wheat genotypes. It included the Chinese variety Ning0604, carrying a quantitative trait locus (QTL) on chromosome 5B associated with a higher root dry biomass, and three elite German varieties, Elixer, Genius, and Leandrus. Experiment 2 compared near-isogenic lines (NIL) of the three elite varieties, each containing introgressions of the QTL on chromosome 5B linked to root dry mass. In both experiments, nitrogen partitioning was tracked via isotope discrimination after fertilization with 5 Atom % 15N-labeled KNO3-. RESULTS: In experiment 1 the quantification by 15N isotope discrimination revealed significantly (p < 0.05) higher nitrogen derived from fertilizer in the root organ for Ning0604 than those of the three German varieties. In experiment 2, two out of three NILs showed a significantly (p < 0.05) higher uptake of N derived from fertilizer than their respective recipient line under well-watered conditions. Furthermore, significantly lower transpiration rates (p < 0.1) were observed in one NIL compared to its respective recipient. CONCLUSIONS: The combination of the DroughtSpotter facility coupled with 15N tracer-based tracking of N uptake and remobilization extends the insight into the impact of genetically altered root biomass on wheat NUE and WUE under different water availability scenarios. The study shows the potential for how a modified genetic constitution of the locus on wheat chromosome 5B can reduce transpiration and enhance N uptake. The dependence of the observations on the recipient and water availability suggests a need for further research to investigate the interaction with genetic background traits.


Subject(s)
Nitrogen , Quantitative Trait Loci , Quantitative Trait Loci/genetics , Triticum/genetics , Droughts , Ecosystem , Fertilizers , Plant Breeding , Water , Chromosomes , Isotopes
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