Genome-wide Approach Research Articles

Genome-Wide Association Study of Exercise Addiction Among Elite Wrestlers

Background: Exercise addiction, marked by an inability to control exercise and associated with distress that clinically impairs daily activities, is a significant but underrecognized issue in physical activity and health. While its physiological, psychological, and behavioral aspects have been studied, the genetic basis of exercise addiction remains poorly understood, requiring further investigation. The present study conducted a genome-wide association study of exercise addiction among elite Turkish wrestlers. Methods: The sample comprised 67 male wrestlers (34 freestyle wrestlers and 33 Greco-Roman wrestlers). Exercise addiction was assessed using the Exercise Addiction Scale. Whole-genome genotyping was performed using DNA microarray. Results: Using a genome-wide approach (p < 1.0 × 10−⁵), we identified six suggestively significant single-nucleotide polymorphisms (SNPs) associated with exercise addiction status. Of these, the high-addiction alleles of five SNPs (PRDM10 rs74345126, near PTPRU rs72652685, HADHB rs6745226, XIRP2 rs17614860, and near GAREM2 rs1025542) have previously been associated with an increased risk of mental health disorders such as anxiety and depression or higher levels of physical activity. We also examined potential associations between the genetic markers previously linked to addiction-related traits such as obsessive–compulsive disorder and cigarette smoking, and personality traits linked to negative emotions including neuroticism. Using this candidate gene approach (p < 0.05), we identified three additional SNPs associated with exercise addiction in the same direction of association (DEFB135 rs4841662, BCL11A rs7599488, and CSRNP3 rs1551336). Conclusions: The present study provides preliminary evidence for the genetic basis of exercise addiction, highlighting specific SNPs that may play a role in the development of this condition among elite wrestlers.

Genome-wide association studies to assess genetic factors controlling cucumber resistance to CABYV and CMV in crop fields and the attractiveness for their Aphis gossypii vector”

Abstract Cucumber crops face high pressure from pathogens, including various viral species. Mapping quantitative trait loci (QTL) for vegetable resistance to viruses has primarily been conducted after mechanical inoculation in controlled environments, but not in crop field conditions. Moreover, viruses which cannot be mechanically inoculated, e.g. the cucurbit aphid-borne yellows virus (CABYV), have been overlooked in resistance studies. Here we aimed to identify QTLs reducing epidemics of two prevalent cucumber viruses: CABYV and the cucumber mosaic virus (CMV). We evaluated the resistance of 256 elite cucumber lines and landraces in crop field conditions by screening for the presence of both viruses six-times during the season. We mapped twelve QTLs reducing CABYV epidemics and seven QTLs reducing CMV epidemics by combining multi-loci genome-wide association studies (GWAS) and local score approach analyses. We also examined the attractiveness of this cucumber panel for Aphis gossypii, a major cucumber virus vector. We identified five QTLs that reduced the attractiveness, including one co-localizing with a QTL reducing CABYV epidemics. Interestingly, some accessions deemed CMV-resistant after mechanical inoculation in controlled environments showed high infection rates in crop field conditions. Only one QTL for CMV resistance was detected in both conditions, indicating that these phenotypes are regulated by independent QTLs. Local linkage disequilibrium study findings suggested that certain QTLs reducing epidemics were introduced early into elite lines through serendipity or selection. QTLs could be pyramided with other low effect QTLs through genomic selection to obtain cucumber cultivars with enhanced field resistance to viruses.

The mutational landscape of Staphylococcus aureus during colonisation

Staphylococcus aureus is an important human pathogen and a commensal of the human nose and skin. Survival and persistence during colonisation are likely major drivers of S. aureus evolution. Here we applied a genome-wide mutation enrichment approach to a genomic dataset of 3060 S. aureus colonization isolates from 791 individuals. Despite limited within-host genetic diversity, we observed an excess of protein-altering mutations in metabolic genes, in regulators of quorum-sensing (agrA and agrC) and in known antibiotic targets (fusA, pbp2, dfrA and ileS). We demonstrated the phenotypic effect of multiple adaptive mutations in vitro, including changes in haemolytic activity, antibiotic susceptibility, and metabolite utilisation. Nitrogen metabolism showed the strongest evidence of adaptation, with the assimilatory nitrite reductase (nasD) and urease (ureG) showing the highest mutational enrichment. We identified a nasD natural mutant with enhanced growth under urea as the sole nitrogen source. Inclusion of 4090 additional isolate genomes from 731 individuals revealed eight more genes including sasA/sraP, darA/pstA, and rsbU with signals of adaptive variation that warrant further characterisation. Our study provides a comprehensive picture of the heterogeneity of S. aureus adaptive changes during colonisation, and a robust methodological approach applicable to study in host adaptive evolution in other bacterial pathogens.

Genome-Wide Approach Identifies Natural Large-Fragment Deletion in ASFV Strains Circulating in Italy During 2023.

African swine fever (ASF), characterized by high mortality rates in infected animals, remains a significant global veterinary and economic concern, due to the widespread distribution of ASF virus (ASFV) genotype II across five continents. In this study, ASFV strains collected in Italy during 2022-2023 from two geographical clusters, North-West (Alessandria) and Calabria, were fully sequenced. In addition, an in vivo experiment in pigs was performed. Complete genomic sequencing of 30 strains revealed large-fragment deletions and translocations. In Alessandria, five samples showed two different deletions in the 5' genomic region: a ~4340 bp deletion (positions ~9020-13,356 in Georgia 2007/1) in four samples and a 2162 bp deletion (positions 17,837-19,998) in one sample. Another strain showed a truncation of 1950 bp at the 3' end. In Calabria, strains showed a 5137 bp deletion (positions 10,755-15,891) and ~2 kb truncations in the 3' region. Two strains showed a translocation from the region 1-2244 to positions 188,631-190,584. In vivo characterization of the deleted strain 22489.4_2312/RC/2023 revealed identical disease progression to the wild-type strain, with severe ASF symptoms in inoculated pigs. This study is the first to report natural deleted strains of ASFV in Italy, revealing unique genomic deletions distinct from those in previously known strains.

Statistical examination of shared loci in neuropsychiatric diseases using genome-wide association study summary statistics

Continued methodological advances have enabled numerous statistical approaches for the analysis of summary statistics from genome-wide association studies. Genetic correlation analysis within specific regions enables a new strategy for identifying pleiotropy. Genomic regions with significant ‘local’ genetic correlations can be investigated further using state-of-the-art methodologies for statistical fine-mapping and variant colocalisation. We explored the utility of a genome-wide local genetic correlation analysis approach for identifying genetic overlaps between the candidate neuropsychiatric disorders, Alzheimer’s disease (AD), amyotrophic lateral sclerosis (ALS), frontotemporal dementia, Parkinson’s disease, and schizophrenia. The correlation analysis identified several associations between traits, the majority of which were loci in the human leukocyte antigen region. Colocalisation analysis suggested that disease-implicated variants in these loci often differ between traits and, in one locus, indicated a shared causal variant between ALS and AD. Our study identified candidate loci that might play a role in multiple neuropsychiatric diseases and suggested the role of distinct mechanisms across diseases despite shared loci. The fine-mapping and colocalisation analysis protocol designed for this study has been implemented in a flexible analysis pipeline that produces HTML reports and is available at: https://github.com/ThomasPSpargo/COLOC-reporter.

Canonical androgen response element motifs are tumor suppressive regulatory elements in the prostate

The androgen receptor (AR) is central in prostate tissue identity and differentiation, and controls normal growth-suppressive, prostate-specific gene expression. It also drives prostate tumorigenesis when hijacked for oncogenic transcription. The execution of growth-suppressive AR transcriptional programs in prostate cancer (PCa) and the potential for reactivation remain unclear. Here, we use a genome-wide approach to modulate canonical androgen response element (ARE) motifs—the classic DNA binding elements for AR—to delineate distinct AR transcriptional programs. We find that activating these AREs promotes differentiation and growth-suppressive transcription, potentially leading to AR+ PCa cell death, while ARE repression is tolerated by PCa cells but deleterious to normal prostate cells. Gene signatures driven by ARE activity correlate with improved prognosis and luminal phenotypes in PCa patients. Canonical AREs maintain a normal, lineage-specific transcriptional program that can be reengaged in PCa cells, offering therapeutic potential and clinical relevance.

Genome-Wide Association Mapping of Macronutrient Mineral Accumulation in Wheat (Triticum aestivum L.) Grain

The focus on increasing wheat (Triticum aestivum L.) grain yield at the expense of grain quality and nutrient accumulation can lead to shortages in macronutrient minerals, which are dangerous for human health. This is important, especially in nations where bread wheat is used in most daily dietary regimens. One efficient way to guarantee nutritional security is through biofortification. A genome-wide association mapping approach was used to investigate the genetic basis of the differences in macronutrient mineral accumulation in wheat grains. N, P, K, Na, Ca, and Mg concentrations were measured after a panel of 200 spring wheat advanced lines from the Wheat Association Mapping Initiative were cultivated in the field. The population exhibited a wide range of natural variations in macronutrient minerals. The minerals were found to have strong positive correlations except for magnesium, which had negative correlation patterns with N, P, and K. Furthermore, there were negative correlations between N and each of Ca and Na. Remarkably, genotypes with large yields contained moderate levels of critical metals. Of the 148 significant SNPs above −log10(P) = 3, 29 had −log10(P) values greater than 4. Four, one, and nineteen significant SNPs with a −log10(P) between 4 and 5.8 were associated with N and mapped on chromosomes 1A, 1B, and 1D, respectively. Three significant SNPs on chromosome A3 were associated with K. Two significant SNPs were associated with Ca and Na and mapped on chromosomes B3 and A4, respectively. Our findings offer crucial information about the genetic underpinnings of nutritional mineral concentration augmentation, which can guide future breeding research to enhance human nutrition.

Clinical Features, Biochemistry, Imaging, and Treatment Response in a Single-Center Cohort With Coenzyme Q10 Biosynthesis Disorders.

Disorders of coenzyme Q10 (CoQ10) biosynthesis comprise a group of 11 clinically and genetically heterogeneous rare primary mitochondrial diseases. We sought to delineate clinical, biochemical, and neuroimaging features of these disorders, together with outcomes after oral CoQ10 supplementation and the utility of peripheral blood mononuclear cell (PBMNC) CoQ10 levels in monitoring therapy. This was a retrospective cohort study, registered as an audit at a specialist pediatric hospital (Registration Number: 3318) of 14 patients with genetically confirmed CoQ10 biosynthesis deficiency, including 13 previously unreported cases. We show that oral doses of CoQ10 up to 70 mg/kg/d were needed to ameliorate neurologic features. Additional idebenone was required to control seizures in some cases, and 3 children with neonatal-onset neurologic disease died in early childhood despite receiving high-dose oral CoQ10 from birth. We also demonstrate that early diagnosis and treatment of CoQ10 deficiency with oral supplementation (30 mg/kg/d) can reverse renal manifestations and can completely prevent kidney disease over 10 years of follow-up. PBMNC CoQ10 levels increased after oral CoQ10 supplementation, demonstrating absorption of exogenous CoQ10 into the bloodstream. An early genome-wide diagnostic approach is needed for expeditious diagnosis of CoQ10 biosynthesis disorder because our study demonstrates that there are no pathognomonic blood, muscle, or imaging biomarkers of these diseases. Our findings indicate that earlier diagnosis and treatment with high-dose CoQ10 is key in halting progression of kidney disease or preventing it altogether. This study uses serial PBMNC CoQ10 levels to monitor therapy. Patients with genetically confirmed CoQ10 biosynthesis disorder should receive high-dose oral CoQ10 as soon as possible after presentation, regardless of genetic cause, to prevent disease progression, but parents of children with neonatal or infantile neurologic presentations should be counseled about the poor prognosis.

Genome-wide identification, classification, and expression profiling of the aldehyde dehydrogenase gene family in pepper.

Pepper (Capsicum annuum L.) is one of the most significant vegetable crops worldwide which is known for its pungency and nutritional value. The aldehyde dehydrogenase (ALDH) superfamily encompasses enzymes critical for the detoxification of toxic aldehydes into non-toxic carboxylic acids. A comprehensive genome-wide approach in pepper identified a total of 27 putative ALDH genes grouped into ten families based on the criteria of the ALDH gene nomenclature committee. Both segmental and tandem duplication assisted in the enhancement of CaALDH gene family members. The identified CaALDH members were found to be more closely related to the dicot plants, however, the members were distributed across the phylogenetic tree suggesting the pre-eudicot-monocot separation of the ALDH superfamily members. The gene structure and protein domain were found to be mostly conserved in separate phylogenetic classes, indicating that each family played an important role in evolution. Expression analysis revealed that CaALDHs were expressed in various tissues, developmental stages, and in response to abiotic stresses, indicating that they can play roles in plant growth, development, and stress adaptation. Interestingly, the majority of the CaALDH genes were found to be highly responsive to salinity stress, and only the CaALDH11A1 transcript showed upregulation in cold stress conditions. The presence of cis-acting elements in the promoter region of these genes might have a significant role in abiotic stress tolerance. Overall, these findings add to the current understanding, evolutionary history, and contribution of CaALDHs in stress tolerance, and smooth the path of further functional validation of these genes.

Genome-Wide Approach of Gene-Nutrient Intake Interaction Study for Essential Hypertension in a Large Korean Cohort (KoGES).

Background/Objectives: There is limited evidence on gene-nutrient interaction associated with hypertension (HTN). We examined interactions between genotypes and various nutrients that influenced high blood pressure (BP). Methods: Data were obtained from a total of 50,808 participants from the Korean Genome and Epidemiology Study (KoGES). Dietary intake was assessed by a food frequency questionnaire, and dietary reference intakes (DRIs) were set. We performed genome-wide association analyses (GWAS) and subsequent interaction analyses with genome-wide significant SNPs to identify genomic loci that interact with specific nutrients associated with HTN. Results: We identified one locus near the CUB and Sushi Multiple Domains 1 (CSMD1) gene that showed interaction with dietary iron and vitamin B6 (Vit.B6) intake and significantly influenced HTN risk. Among the individuals consuming iron above DRI (9.5 mg/day for men, 9.25 mg/day for women), carriers of the rs13282715 minor allele (A) at 8p23.2 showed a lower risk of HTN than those who did not (odds ratio [OR] 0.723, 95% confidence interval [CI] (0.644-0.813), p-value 4.858 × 10-8; interaction p-value 1.336 × 10-3). Among the individuals consuming Vit.B6 above DRI (1.5 mg/day for men, 1.4 mg/day for women), carriers of the same variant rs13282715 minor allele (A) also showed a lower risk of HTN (OR 0.733, 95% CI 0.733 (0.656-0.819), p-value 4.121 × 10-8; interaction p-value 7.183 × 10-4). Conclusions: We identified a novel gene-nutrient interaction regarding dietary iron and Vit.B6 intake affecting the risk of HTN in Korean adults. This suggests individuals with the variant may benefit from lower HTN risk from dietary intervention of iron and Vit.B6 intake. Further studies with larger diverse populations are warranted to validate our findings.

Hidden invaders: intraspecific cryptic invasion and hybridization of Dolichoderus thoracicus (Hymenoptera: Formicidae) in Taiwan.

Biological invasions pose substantial threats to global biodiversity, agriculture, and ecological stability. Among these, intraspecific cryptic invasions, characterized by the spread of nonnative genotypes within a species, present unique challenges for detection and management. Despite the well-documented influence of invasive ants on ecosystems, instances of intraspecific cryptic ant invasions have rarely been documented. This study focused on the black cocoa ant, Dolichoderus thoracicus (Smith 1860), which has been increasingly reported as a pest in Taiwan over the past decade. In this study, we utilized a genome-wide approach employing multiplexed inter-simple sequence repeats genotyping by sequencing to identify single nucleotide polymorphisms across the D. thoracicus populations, elucidating the variations in the genetic population structure of the species in Taiwan. Our findings confirmed the occurrence of intraspecific cryptic invasions, demonstrating the coexistence of native and nonnative lineages, along with potential hybridization events between them. This study underscores the critical role of comprehensive genetic analysis in uncovering the complex dynamics of species invasions.

Abstract A050: Early detection of liver cancer from diverse populations using cfDNA fragmentome and protein biomarkers

Abstract Hepatocellular carcinoma (HCC) is a leading cause of cancer death world-wide. In the US, liver cancer has increased in incidence and mortality due to a growing population from South and Central America, which faces higher risk of disease in part due to aflatoxin exposure. Recently, we showed that the DELFI (DNA evaluation of fragments for early interception) approach using genome-wide cell free DNA (cfDNA) fragmentation profiles and machine learning can be used for detection of liver and other cancers. Having previously demonstrated that a DELFI classifier accurately detects HCC in populations from the US and Hong Kong, we evaluated the classifier in other clinically relevant cohorts worldwide. Here we show that approach generalizes to diverse populations, and that including other genomic and protein features from the same blood draw improves performance. We examined plasma samples from 377 individuals, including 244 individuals with HCC and 133 without cancer, including 85 with cirrhosis. Plasma samples were collected from individuals with or without HCC in a case-control study in Guatemala (n=203) and from a prospective collection in Romania (n=174) and cfDNA was analyzed by whole- genome sequencing at ∼10x coverage. The median DELFI scores using a locked classifier (Foda et al., Cancer Discovery, 2023) were higher in both cohorts for patients with cancer across all stages compared to individuals without cancer, regardless of the presence of cirrhosis. Using the locked model with a threshold that corresponded to 80% specificity in prior work, DELFI detected individuals with HCC with sensitivities of 90% and 69% in the two cohorts at specificities of 92% and 86%, respectively. For early-stage HCC within Milan Criteria for liver transplantation, sensitivities were 85% in the case-control cohort and 64% in the prospective cohort. In these cohorts, the fixed DELFI model outperformed AFP at the clinically used threshold of 20 ng/mL with a sensitivity in the combined cohorts of 78% at 91% specificity, compared to 63% sensitivity at 91% specificity for AFP. A combined approach using either DELFI at a threshold that corresponded to a 90% specificity in our previous study or AFP at the clinical threshold resulted in 82% sensitivity (74% in early stage) at 92% specificity and was superior to estimates of AFP and ultrasound for early-stage disease (63% sensitivity at 84% specificity). Individuals who tested positive with DELFI had a significantly shorter overall survival (p=0.002, log rank test), even amongst individuals at the earliest stage, while AFP alone did not stratify survival for patients with early-stage disease. Single-molecule analyses from low coverage WGS of cfDNA revealed genome-wide mutational profiles that were similar to those of HCC and in individuals from Guatemala that were characteristic of aflatoxin exposure. Overall, this work provides insight into the origins of cfDNA in populations at risk for HCC and validates our genome-wide fragmentome approach for non-invasive cancer detection that may facilitate liver cancer screening. Citation Format: Zachariah H Foda, Daniel Bruhm C Bruhm, Akshaya V Annapragada, Shashikant Koul, Sarah Short, Keerti Boyapati, Adrianna Bartolomucci, Vilmos Adleff, Nicholas A Vulpescu, Hope Orjuela, Andrei Sorop, Razvan Iacob, Liana Gheorghe, Simona Dima, Katherine A McGlynn, Manuel Ramírez-Zea, Jillian Phallen, John Groopman, Robert B Sharpf, Victor E Velculescu. Early detection of liver cancer from diverse populations using cfDNA fragmentome and protein biomarkers [abstract]. In: Proceedings of the AACR Special Conference: Liquid Biopsy: From Discovery to Clinical Implementation; 2024 Nov 13-16; San Diego, CA. Philadelphia (PA): AACR; Clin Cancer Res 2024;30(21_Suppl):Abstract nr A050.

Genome-wide selection of potential target candidates for RNAi against Nilaparvata lugens

BackgroundNilaparvata lugens is one of the most destructive pests of rice. RNAi-based N. lugens control offers one alternative strategy to traditional chemical insecticides. However, selection of potential target for RNAi against N. lugens remains a major challenge. Only two target genes for nuclear transgenic N. lugens-resistant plants have been screened. Importantly, only one or few potential target genes against N. lugens were screened every time by knowledge of essential genes from model organisms in previous study.ResultsHere, in silico genome-wide selection of potential target genes against N. lugens through homology comparison was performed. Through genome synteny comparisons, about 3.5% of Drosophila melanogaster genome was found to have conserved genomic synteny with N. lugens genome. By using N. lugens proteins to search D. melanogaster homologs defining lethal or sterile phenotype, 358 N. lugens genes were first screened as putative target genes. Transgenic rice lines expressing dsRNA of randomly selected gene (NlRan or NlSRP54) from 358 putative target genes enhanced resistance to N. lugens. After expression check and safety check, 115 N. lugens genes were screened as potential target candidates.ConclusionThe combined efforts in this study firstly provide one in silico genome-wide homology-based screening approach for RNAi-based target genes against N. lugens, which not only offer one new opportunity to batch select potential target candidates in pests of interest, but also will facilitate the selection of RNAi target in many pest species by providing more than one hundred potential target candidates.

Appraising the life-course impact of Epstein-Barr virus exposure and its genetic signature on periodontitis.

Periodontitis arises from a multifaceted interplay of environmental variables and genetic susceptibility, where microbial infection plays an indispensable part. Epstein-Barr virus (EBV) exposure has long been considered associated with periodontitis activity; however, the causal relationship and genetic connection between them remain unknown. Within a life-course context, our study employed comprehensive Mendelian randomization (MR) methods, including univariable, multivariable, Bayesian model averaging, and reverse MR, to investigate the causal association between EBV exposure and periodontitis. Additionally, linkage disequilibrium score regression and colocalization analysis were utilized to assess the cross-trait genetic correlations, followed by transcriptome-wide association and enrichment analysis to discern the genetic-phenotypic biological profiles. Heightened levels of EBV antibodies, particularly early antigen diffuses (which serve as indicators of early infection or reactivation), are associated with an increased risk of periodontitis (odds ratio [OR]: 1.27 [1.09-1.47],p=6.05×10-3) and demonstrate a significant genetic correlation (p=4.11×10-3). This pathogenesis may involve the high-confidence causal gene RNASEK located in 17p13.1. Genetically predicted early-life anti-EBV immunoglobulin G (IgG) levels are correlated to a reduced periodontitis risk (OR: 0.89 [0.82-0.97],p=1.76×10-3). The present study highlights the impact of life-course EBV exposure and its genetic hallmark on periodontitis, providing novel perspectives into the underlying pathogenesis and management strategies for EBV-related periodontitis. These findings underscore diverse clinical and public health implications, encompassing antiviral therapies, viral vaccination strategies, and tailored interventions for individualized periodontitis management. Further research is required to validate and expand upon our findings. Periodontitis is a chronic inflammatory disease driven by interactions between microbial pathogens and the host immune system. While bacteria have traditionally been the focus of research, recent studies highlight the significance of virus-bacteria interactions, particularly the role of Epstein-Barr virus (EBV)-a herpesvirus infecting over 90% of the global population-in the development of periodontitis. However, the underlying causal and genetic mechanisms remain unclear. Our study employed genome-wide multi-omics approaches to investigate the link between EBV exposure and periodontitis. We found that recent EBV infection or reactivation increases the risk of periodontitis, whereas early-life exposure, possibly enabling immune resistance, may reduce it. Essential genes were identified as potential mediators, including CRTC3-AS1, HLA-DQA1, and RNASEK. These findings provide novel insights into the EBV-periodontitis connection. For example, viral testing and control could benefit patients unresponsive to standard bacterial treatments, and early viral exposure via vaccination might reduce the risk of periodontitis. Further clinical studies are required to elucidate these underlying mechanisms and the contribution of virus-bacteria interactions.

Unlocking the role of novel primary/di-amine oxidases in crop improvement: Tissue specificity leads to specific roles connected to abiotic stress, hormone responses and sensing nitrogen

Genetic improvements of solanaceous crops for quality and stress responsive traits are needed because of the central role vegetables and fruits have in providing nutrients to human diets. Copper amine oxidase (CuAO) encoding genes involved in metabolism of primary/di-amine nitrogenous compounds, play a role in balancing internal nitrogen (N) pools especially when external N supply fluctuates during growth, development and environmental stresses. In the present study, we investigated the occurrence, molecular evolution and possible role(s) of these unknown genes in tomato crops. Multiple genome-wide bioinformatics approaches led to the identification of eight bona fide CuAO genes (SlCuAO1–SlCuAO8) in the tomato genome with gene numbers like those in Arabidopsis and rice indicating their conserved functional relevance with a tandemly duplicated SlCuAO6-SlCuAO7 pair at chr.9. A conserved intron-exon size and phase distribution for SlCuAO2, 3, 4 pairs are similar to a recently identified single duckweed SpCuAO1 orthologue gene indicating its evolutionary conservation. Synteny analysis showed their closest association to Arabidopsis and but not with rice. Transcriptome data indicated that gene expression for about six genes (SlCuAO1, 2, 3, 4, 6, 7) is root specific, fruit specific for SlCuAO5 and flower specific for SlCuAO8 thus indicating amine oxidation is variable across tissues with a prominance in the root tissue. The majority of CuAO genes are negatively regulated by methyl jasmonate. Positive regulation, however, involves CuAO3/8. Transcript analysis of the ethylene-deficient transgenic lines indicated that ethylene is required for activation of SlCuAO4. CuAO4 and CuAO5 exhibited most significant tissues-independent gene expression responses across various nitrogen regimes. Drought, heat and N stress identified CuAO5 as an overlapping highly expressed gene that corroborates with putrescine accumulation for free and conjugated forms with an opposite abundance of bound forms. Taken together our study highlights new insights into the roles of copper amine oxidation genes and identifies CuAO5 as a multiple stress induced gene that can be used in genetic improvement programs for combining heat, drought and nitrogen use efficiency related traits.

Prenatal risk assessment of Xp21.1 duplication involving the DMD gene by optical genome mapping.

Structural variants (SVs) of unknown significance are great challenges for prenatal risk assessment, especially when involving dose-sensitive genes such as DMD The pathogenicities of 5'-terminal DMD duplications in the database remain controversial. Four prenatal cases with Xp21.1 duplications were identified by routine prenatal genomic testing, encompassing the 5'-UTR to exons 1-2 in family 1 and family 2, and to exons 1-9 in family 3. The duplication in family 4 was non-contiguous covering the 5'-UTR to exon 1 and exons 3-7. All were traced to unaffected males in the family pedigrees. A new genome-wide approach of optical genome mapping was performed in families 1, 2, and 3 to delineate the breakpoints and orientation of the duplicated fragments. The extra copies were tandemly inserted into the upstream of DMD, preserving the integrity of ORF from the second copy. The pathogenicities were thus reclassified as likely benign. Our data highlight the importance of structural delineation by optical genome mapping in prenatal risk assessment of incidentally identified SVs involving DMD and other similar large dose-sensitive genes.

Antimicrobial Peptide with a Bent Helix Motif Identified in Parasitic Flatworm Mesocestoides corti.

The urgent need for antibiotic alternatives has driven the search for antimicrobial peptides (AMPs) from many different sources, yet parasite-derived AMPs remain underexplored. In this study, three novel potential AMP precursors (mesco-1, -2 and -3) were identified in the parasitic flatworm Mesocestoides corti, via a genome-wide mining approach, and the most promising one, mesco-2, was synthesized and comprehensively characterized. It showed potent broad-spectrum antibacterial activity at submicromolar range against E. coli and K. pneumoniae and low micromolar activity against A. baumannii, P. aeruginosa and S. aureus. Mechanistic studies indicated a membrane-related mechanism of action, and circular dichroism spectroscopy confirmed that mesco-2 is unstructured in water but forms stable helical structures on contact with anionic model membranes, indicating strong interactions and helix stacking. It is, however, unaffected by neutral membranes, suggesting selective antimicrobial activity. Structure prediction combined with molecular dynamics simulations suggested that mesco-2 adopts an unusual bent helix conformation with the N-terminal sequence, when bound to anionic membranes, driven by a central GRGIGRG motif. This study highlights mesco-2 as a promising antibacterial agent and emphasizes the importance of structural motifs in modulating AMP function.

NUMB dysfunction defines a novel mechanism underlying hyperuricemia and gout

Defective renal excretion and increased production of uric acid engender hyperuricemia that predisposes to gout. However, molecular mechanisms underlying defective uric acid excretion remain largely unknown. Here, we report a rare genetic variant of gout-unprecedented NUMB gene within a hereditary human gout family, which was identified by an unbiased genome-wide sequencing approach. This dysfunctional missense variant within the conserved region of the NUMB gene (NUMBR630H) underwent intracellular redistribution and degradation through an autophagy-dependent mechanism. Mechanistically, we identified the uric acid transporter, ATP Binding Cassette Subfamily G Member 2 (ABCG2), as a novel NUMB-binding protein through its intracellular YxNxxF motif. In polarized renal tubular epithelial cells (RTECs), NUMB promoted ABCG2 trafficking towards the apical plasma membrane. Genetic loss-of-function of NUMB resulted in redistribution of ABCG2 in the basolateral domain and ultimately defective excretion of uric acid. To recapitulate the clinical situation in human gout patients, we generated a NUMBR630H knock-in mouse strain, which showed marked increases of serum urate and decreased uric acid excretion. The NUMBR630H knock-in mice exhibited clinically relevant hyperuricemia. In summary, we have uncovered a novel NUMB-mediated mechanism of uric acid excretion and a functional missense variant of NUMB in humans, which causes hyperuricemia and gout.

Enhancers in Plant Development, Adaptation, and Evolution.

Understanding plant responses to developmental and environmental cues is crucial for studying morphological divergence and local adaptation. Gene expression changes, governed by cis-regulatory modules (CRMs) including enhancers, are a major source of plant phenotypic variation. However, while genome-wide approaches have revealed thousands of putative enhancers in mammals, far fewer have been identified and functionally characterized in plants. This review provides an overview of how enhancers function to control gene regulation, methods to predict DNA sequences that may have enhancer activity, methods utilized to functionally validate enhancers, and the current knowledge of enhancers in plants, including how they impact plant development, response to environment, and evolutionary adaptation.

Genome-Wide Transcriptional Response of Avocado to Fusarium sp. Infection.

The avocado crop is relevant for its economic importance and because of its unique evolutionary history. However, there is a lack of information regarding the molecular processes during the defense response against fungal pathogens. Therefore, using a genome-wide approach in this work, we investigated the transcriptional response of the Mexican horticultural race of avocado (Persea americana var. drymifolia), including miRNAs profile and their possible targets. For that, we established an avocado-Fusarium hydroponic pathosystem and studied the response for 21 days. To guarantee robustness in the analysis, first, we improved the avocado genome assembly available for this variety, resulting in 822.49 Mbp in length with 36,200 gene models. Then, using an RNA-seq approach, we identified 13,778 genes differentially expressed in response to the Fusarium infection. According to their expression profile across time, these genes can be clustered into six groups, each associated with specific biological processes. Regarding non-coding RNAs, 8 of the 57 mature miRNAs identified in the avocado genome are responsive to infection caused by Fusarium, and the analysis revealed a total of 569 target genes whose transcript could be post-transcriptionally regulated. This study represents the first research in avocados to comprehensively explore the role of miRNAs in orchestrating defense responses against Fusarium spp. Also, this work provides valuable data about the genes involved in the intricate response of the avocado during fungal infection.