RXR nuclear receptor signaling modulates lipid metabolism and triggers lysosomal clearance of alpha-synuclein in neuronal models of synucleinopathy.

Disease-modifying strategies for Parkinson disease (PD), the most common synucleinopathy, represent a critical unmet medical need. Accumulation of the neuronal protein alpha-synuclein (αS) and abnormal lipid metabolism have each been implicated in PD pathogenesis. Here, we elucidate how retinoid-X-receptor (RXR) nuclear receptor signaling impacts these two aspects of PD pathogenesis. We find that activated RXR differentially regulates fatty acid desaturases, significantly reducing the transcript levels of the largely brain-specific desaturase SCD5 in human cultured neural cells and PD patient-derived neurons. This was associated with reduced perilipin-2 protein levels in patient neurons, reversal of αS-induced increases in lipid droplet (LD) size, and a reduction of triglyceride levels in human cultured cells. With regard to αS proteostasis, our study reveals that RXR agonism stimulates lysosomal clearance of αS. Our data support the involvement of Polo-like kinase 2 activity and αS S129 phosphorylation in mediating this benefit. The lowering of cellular αS levels was associated with reduced cytotoxicity. Compared to RXR activation, the RXR antagonist HX531 had the opposite effects on LD size, SCD, αS turnover, and cytotoxicity, all supporting pathway specificity. Together, our findings show that RXR-activating ligands can modulate fatty acid metabolism and αS turnover to confer benefit in cellular models of PD, including patient neurons. We offer a new paradigm to investigate nuclear receptor ligands as a promising strategy for PD and related synucleinopathies.

Gapless genome assembly and epigenetic profiles reveal gene regulation of whole-genome triplication in lettuce.

BACKGROUND: Lettuce, an important member of the Asteraceae family, is a globally cultivated cash vegetable crop. With a highly complex genome (∼2.5 Gb; 2n = 18) rich in repeat sequences, current lettuce reference genomes exhibit thousands of gaps, impeding a comprehensive understanding of the lettuce genome. FINDINGS: Here, we present a near-complete gapless reference genome for cutting lettuce with high transformability, using long-read PacBio HiFi and Nanopore sequencing data. In comparison to stem lettuce genome, we identify 127,681 structural variations (SVs, present in 0.41 Gb of sequence), reflecting the divergence of leafy and stem lettuce. Interestingly, these SVs are related to transposons and DNA methylation states. Furthermore, we identify 4,612 whole-genome triplication genes exhibiting high expression levels associated with low DNA methylation levels and high N6-methyladenosine RNA modifications. DNA methylation changes are also associated with activation of genes involved in callus formation. CONCLUSIONS: Our gapless lettuce genome assembly, an unprecedented achievement in the Asteraceae family, establishes a solid foundation for functional genomics, epigenomics, and crop breeding and sheds new light on understanding the complexity of gene regulation associated with the dynamics of DNA and RNA epigenetics in genome evolution.

Urethral multiplicity in boys: systematic review of case reports and case series from the last 15 years.

Introduction: Urethral multiplicity is a rare congenital anomaly characterized by the presence of two or more urethral channels. It is more common in males and can cause double urinary stream, incontinence, obstruction, and recurrent urinary infections. Diagnosis is difficult due to diverse clinical manifestations. Implementing an evidence-based treatment plan is challenging due to the need for more concise and informative summary publications. Our paper provides a comprehensive review of the management of this pathology and might serve as a valuable resource for pediatric urologists and specialists in the field. Methods: A comprehensive search in four electronic databases, PubMed®, PubMed Central® (PMC), Scopus, and Clarivate Analytics's Web of Science (WoS), was conducted to identify case reports and series published between 2008 and 2023 on urethral multiplicities. The quality of the articles was assessed using qualified instruments. Covidence® tool-guided synthesis was followed by individual patient data extraction. Further classifications and analysis were made using Microsoft Excel®. Results: Out of the 90 papers included in the review, 62 were case presentations, and 28 were case series. We found 250 boys with urethral multiplicity. Based on Effman's classification, there were 38 cases of type I (15.3%), 21 type IIA1 (8.4%), 55 type IIA2 (22.1%), 91 type IIA2Y (36.5%), 4 type IIB (1.6%), and 6 type III (2.4%) urethral duplications. There were 19 cases of prepubic sinuses (7.6%), 9 triplications (3.6%), and 6 unknown forms (2.4%). We have provided data for each type, including clinical presentation, investigations, surgical management, and outcomes. Conclusions: Urethral multiplicities are a rare and varied group of malformations that require high-quality imaging examination for successful management. Treatment is specific to each patient and may depend on the surgeon's preference or skill. Systematic Review Registration: https://www.crd.york.ac.uk/prospero/display_record.php?ID = CRD42023471685, identifier (CRD42023471685).

Alpha globin gene alterations modifying the phenotype of homozygous beta thalassaemia.

The phenotype of ß-thalassemia varies widely. The primary determinant is the type of beta-globin gene mutation; however, there are secondary and tertiary modifiers also as associated alpha mutations, polymorphisms, as well as coinheritance of mutations affecting other related systems. Co-inheritance of alpha thalassemia mutations is known to ameliorate the severity of HbE-ß thalassemia. However, the role of alpha globin gene alterations (deletions and triplication) is not well illustrated in homozygous ß-thalassemia. Here we evaluated the role of alpha globin gene alterations in 122 ß-thalassemia patients having IVS1-5 (G > C) homozygous mutation. ß-thalassemia mutations were detected by ARMS PCR and alpha mutations by GAP-PCR. Gene expression by qRT-PCR. Out of 122 cases, 15 patients had alpha 3.7 triplications (ααα3.7anti), 24 had alpha 3.7 kb deletion (-α3.7) mutation and three patients had 4.2 kb deletion (-α4.2). Patients were divided into two groups, requiring less than 8 units (NTDT) and more than 8 units (TDT) of blood transfusion per year (≥8U BT/year). The percentage of alpha deletion was significantly (p = 0.0042) high in NTDT (42.1%) as compared with TDT (13.2%). Conversely, the proportion of alpha triplication is high in the TDT as compared with NTDT. Even mean serum ferritin level was found to be significantly high in patients having alpha triplication as compared with those having alpha deletions (p = 0.0184) and normal alpha gene (p = 0.0003). α/ß globin ratio was highest in TDT patients with alpha triplication and lowest in NTDT patients with alpha-del. The results show that concurrent inheritance of alpha gene alterations influences the phenotypic severity of homozygous ß-thalassemia.

Upgraded durian genome reveals the role of chromosome reshuffling during ancestral karyotype evolution, lignin biosynthesis regulation, and stress tolerance.

Durian (Durio zibethinus) is a tropical fruit that has a unique flavor and aroma. It occupies a significant phylogenetic position within the Malvaceae family. Extant core-eudicot plants are reported to share seven ancestral karyotypes that have undergone reshuffling, resulting in an abundant genomic diversity. However, the ancestral karyotypes of the Malvaceae family, as well as the evolution trajectory leading to the 28 chromosomes in durian, remain poorly understood. Here, we report the high-quality assembly of the durian genome with comprehensive comparative genomic analyses. By analyzing the collinear blocks between cacao and durian, we inferred 11 Malvaceae ancestral karyotypes. These blocks were present in a single-copy form in cacao and mainly in triplicates in durian, possibly resulting from a recent whole genome triplication (WGT) event that led to hexaploidization of the durian genome around 20 (17-24) million years ago. A large proportion of the duplicated genes in durian, such as those involved in the lignin biosynthesis module for phenylpropane biosynthesis, are derived directly from whole genome duplication, which makes it an important force in reshaping its genomic architecture. Transcriptome studies have revealed that genes involved in feruloyl-CoA formations were highly preferentially expressed in fruit peels, indicating that the thorns produced on durian fruit may comprise guaiacyl and syringyl lignins. Among all the analyzed transcription factors (TFs), members of the heat shock factor family (HSF) were the most significantly upregulated under heat stress. All subfamilies of genes encoding heat shock proteins (HSPs) in the durian genome appear to have undergone expansion. The potential interactions between HSF Dzi05.397 and HSPs were examined and experimentally verified. Our study provides a high-quality durian genome and reveals the reshuffling mechanism of ancestral Malvaceae chromosomes to produce the durian genome. We also provide insights into the mechanism underlying lignin biosynthesis and heat stress tolerance.

Triplicated middle cerebral arteries (duplicated and ipsilateral accessory) associated with triplicated anterior cerebral arteries (accessory) diagnosed by magnetic resonance angiography.

PURPOSE: To describe a case of duplicated middle cerebral artery (MCA) combined with ipsilateral accessory MCA, forming a triplicated MCA, associated with the accessory anterior cerebral artery (ACA), forming a triplicated A2 segment of the ACA detected incidentally on magnetic resonance (MR) angiography. METHODS: A 70-year-old woman with internal carotid artery (ICA) stenosis at the origin, which was detected by ultrasound, underwent cranial MR imaging and MR angiography of the intracranial region for an evaluation of brain and cerebral arterial lesions. The MR machine was a 3-Tesla scanner. MR angiography was performed using a standard 3-dimensional time-of-flight technique. RESULTS: Multiple ischemic white matter lesions are observed. No significant stenotic lesions were observed in intracranial arteries. The right duplicated MCA was originated from right distal ICA. And main MCA was originated from right ICA bifurcation. Right accessory MCA was arisen from the A2 segment of the right ACA. Thus, the right MCA was triplicated. There was also an accessory ACA forming a triplicated ACA at its A2 segment. These findings were clearly identified on partial volume-rendering (VR) images. CONCLUSION: We herein report a case of triplicated MCA associated with triplicated ACA. MCA variations are relatively rare, and this is the third case of triplicated MCA reported in relevant English-language literature. To identify multiple cerebral arterial variations, creating partial VR images using MR angiographic source images is useful.

Renal Artery Triplication: An Unusual Morphological Variant.

Renal vasculature depicts great morphological variability and clinical significance due to the great number of procedures performed on kidneys. The current imaging report presents a right-sided renal artery (RA) triplication and origin from the abdominal aorta (AA), which was incidentally identified during computed tomography angiography (CTA). The typical RA corresponded to the main hilar artery (MHA), the second RA corresponded to the superior polar artery (SPA), and the third RA corresponded to the inferior polar artery (IPA). RA triplication occurs in 0.9%-4.5% and depicts wide morphological variability. The current report corresponds to one superior polar, one inferior polar, and a main hilar renal artery, which represents a rare morphological type of RA triplication. Kidney transplantation surgery, endoscopic surgery, and renal angiography require adequate knowledge of RAs and their variants to avoid pitfalls and iatrogenic lesions from clinicians.

The clinical value of optical genome mapping in the rapid characterization of RB1 duplication and 15q23q24.2 triplication, for more appropriate prenatal genetic counselling.

BACKGROUND: Despite recent advances in prenatal genetic diagnosis, medical geneticists still face considerable difficulty in interpreting the clinical outcome of copy-number-variant duplications and defining the mechanisms underlying the formation of certain chromosomal rearrangements. Optical genome mapping (OGM) is an emerging cytogenomic tool with proved ability to identify the full spectrum of cytogenetic aberrations. METHODS: Here, we report on the use of OGM in a prenatal diagnosis setting. Detailed breakpoint mapping was used to determine the relative orientations of triplicated and duplicated segments in two unrelated foetuses harbouring chromosomal aberrations: a de novo 15q23q24.2 triplication and a paternally inherited 13q14.2 duplication that overlapped partially with the RB1 gene. RESULTS: OGM enabled us to suggest a plausible mechanism for the triplication and confirmed that the RB1 duplication was direct oriented and in tandem. This enabled us to predict the pathogenic consequences, refine the prognosis and adapt the follow-up and familial screening appropriately. CONCLUSION: Along with an increase in diagnostic rates, OGM can rapidly highlight genotype-phenotype correlations, improve genetic counselling and significantly influence prenatal management.

Genomic and transcriptomic studies on flavonoid biosynthesis in Lagerstroemia indica.

BACKGROUND: Lagerstroemia indica is a widely cultivated ornamental woody shrub/tree of the family Lythraceae that is used as a traditional medicinal plant in East Asia and Egypt. However, unlike other ornamental woody plants, its genome is not well-investigated, which hindered the discovery of the key genes that regulate important traits and the synthesis of bioactive compounds. RESULTS: In this study, the genomic sequences of L. indica were determined using several next-generation sequencing technologies. Altogether, 324.01 Mb sequences were assembled and 98.21% (318.21 Mb) of them were placed in 24 pseudo-chromosomes. The heterozygosity, repeated sequences, and GC residues occupied 1.65%, 29.17%, and 38.64% of the genome, respectively. In addition, 28,811 protein-coding gene models, 327 miRNAs, 552 tRNAs, 214 rRNAs, and 607 snRNAs were identified. The intra- and interspecies synteny and Ks analysis revealed that L. indica exhibits a hexaploidy. The co-expression profiles of the genes involved in the phenylpropanoid (PA) and flavonoid/anthocyanin (ABGs) pathways with the R2R3 MYB genes (137 members) showed that ten R2R3 MYB genes positively regulate flavonoid/anthocyanin biosynthesis. The colors of flowers with white, purple (PB), and deep purplish pink (DPB) petals were found to be determined by the levels of delphinidin-based (Dp) derivatives. However, the substrate specificities of LiDFR and LiOMT probably resulted in the different compositions of flavonoid/anthocyanin. In L. indica, two LiTTG1s (LiTTG1-1 and LiTTG1-2) were found to be the homologs of AtTTG1 (WD40). LiTTG1-1 was found to repress anthocyanin biosynthesis using the tobacco transient transfection assay. CONCLUSIONS: This study showed that the ancestor L. indica experienced genome triplication approximately 38.5 million years ago and that LiTTG1-1 represses anthocyanin biosynthesis. Furthermore, several genes such as LiDFR, LiOMTs, and R2R3 LiMYBs are related to anthocyanin biosynthesis. Further studies are required to clarify the mechanisms and alleles responsible for flower color development.

Triplication of the Sigmoid: A Rare Incidental Finding in Association With an Anorectal Malformation During Colostomy Closure.

This case report presents a rare occurrence of triplication of the sigmoid, an unusual congenital anomaly, in a nine-month-old male with a known history of anorectal malformation. The patient, previously diagnosed with anal atresia and a rectourethral (prostatic) fistula, was admitted for the closure of his divided sigmoidostomy as the final step in correcting his anorectal malformation. Unexpectedly, during the release of the distal stoma, the presence of three distinct bowel lumens was discovered. To discern the native bowel, catheters were introduced into each lumen before proceeding with the excision of the triplicated sigmoid and subsequent stoma closure. This case underscores the complexity of diagnosing and managing unusual GI anomalies in the context of anorectal malformations, emphasizing the challenges encountered during surgical interventions.

Phenotypic and genotypic characterization of 1q21.1 copy number variants: A report of 34 new individuals and literature review.

Recurrent 1q21.1 copy number variants (CNVs) have been associated with a wide spectrum of clinical features, ranging from normal phenotype to moderate intellectual disability, with congenital anomalies and dysmorphic features. They are often inherited from unaffected parents and the pathogenicity is difficult to assess. We describe the phenotypic and genotypic data for 34 probands carrying CNVs in the 1q21.1 chromosome region (24 duplications, 8 deletions and 2 triplications). We also reviewed 89 duplications, 114 deletions and 5 triplications described in the literature, at variable 1q21.1 locations. We aimed to identify the most highly associated clinical features to determine the phenotypic expression in affected individuals. Developmental delay or learning disabilities and neuropsychiatric disorders were common in patients with deletions, duplications and triplications of 1q21.1. Mild dysmorphic features common in these CNVs include a prominent forehead, widely spaced eyes and a broad nose. The CNVs were mostly inherited from apparently unaffected parents. Almost half of the CNVs were distal, overlapping with a common minimal region of 1.2 Mb. We delineated the clinical implications of 1q21.1 CNVs and confirmed that these CNVs are likely pathogenic, although subject to incomplete penetrance and variable expressivity. Long-term follow-up should be performed to each newly diagnosed case, and prenatal genetic counseling cautiously discussed, as it remains difficult to predict the phenotype in the event of an antenatal diagnosis.

Bladder triplication associated with exstrophy variant.

A one-day old full-term female neonate presented with a duplicate bladder and exstrophy variant including a patch of exstrophic or ectopic mucosa, duplicate vagina, uterus, and two complete bladders. We report on the surgical management performed in this case and functional urinary results based on a synchronous urodynamic study of the duplicate bladders. To our knowledge, the occurrence of duplicate bladder exstrophy variant with complete urinary continence has not been previously reported.

Prevalence and genetic analysis of triplicated α-globin gene in Ganzhou region using high-throughput sequencing.

α-globin gene triplication carriers were not anemic in general, while some studies found that α-globin gene triplication coinherited with heterozygous ß-thalassemia may cause adverse clinical symptoms, which yet lacks sufficient evidence in large populations. In this study, we investigated the prevalence and distribution of α-globin gene triplication as well as the phenotypic characteristics of α-globin gene triplication coinherited with heterozygous ß-thalassemia in Ganzhou city, southern China. During 2021-2022, a total of 73,967 random individuals who received routine health examinations before marriage were genotyped for globin gene mutations by high-throughput sequencing. Among them, 1,443 were α-globin gene triplication carriers, with a carrier rate of 1.95%. The most prevalent mutation was αααanti3.7/αα (43.10%), followed by αααanti4.2/αα (38.12%). 42 individuals had coinherited α-globin gene triplication and heterozygous ß-thalassemia. However, they did not differ from the individuals with heterozygous ß-thalassemia and normal α-globin (αα/αα) in terms of mean corpuscular volume (MCV) and mean corpuscular hemoglobin (MCH) levels. In addition, heterogenous clinical phenotypes were found in two individuals with the same genotype. Our study established a database of Ganzhou α-globin gene triplication and provided practical advice for the clinical diagnosis of α-globin gene triplication.

A rare case of right renal ectopia with ureteral triplication in a 37-year-old male: a case report.

Ureteral triplication is one of the least encountered congenital malformations of the upper urinary tract. We report a case of a 37-year-old male patient with right renal ectopia with triplication of the ureter which was diagnosed via computed tomography (CT) urography. This is an intriguing example because, as we discovered after reviewing the literature, the presentation is distinctive.

On-top-plasty reconstruction for thumb triplication.

Thumb triplication is a very rare pattern of radial polydactyly that presents as a more complicated form of thumb. Because of its morphological complexity, treatment often requires surgical ingenuity in addition to the conventional surgical treatment algorithms for duplication. We report the case of thumb triplication on the right hand of a 17-month-old boy. We performed on-top-plasty of the ulnar thumb over the intermediate thumb, and achieved a functional and aesthetic thumb. The technique of on-top-plasty is effective for finger reconstruction that maximizes the use of limited tissue and is widely used for treating hand trauma and congenital hand anomalies. In the present case, on-top-plasty contributed most effectively to creating a sufficiently sized thumb, achieving interphalangeal optimization by joining the extra middle phalanx with the proximal phalanx, and securing the first web space by moving the ulnar thumb laterally.

Transfusion requirements and complication rate in ß-thalassemia intermedia due to heterozygous ß-globin gene mutation and triplicated α-globin genes.

INTRODUCTION: The heterozygous condition for ß-thalassemia mutation associated with an extra functional α-globin gene can produce a Thalassemia Intermedia (TI) phenotype. This genotype is the second in frequency in the French Thalassemia Registry NaThalY that prospectively collects laboratory and clinical data. MATERIALS AND METHODS: The present report analyses transfusion needs, iron overload (ferritin, hepatic and cardiac iron concentrations), and complication rates in 45 patients included in NaThalY and presenting a heterozygous ß0 or ß+ -thalassemia mutation associated with a triplication at HBA locus. This cohort was compared to a cohort of patients with TI due to mutations in the beta-globin gene only and included in the French registry. RESULTS: Patients with an extra functional α-globin gene showed a less severe anemia, lower transfusion needs and lower complication rates than those with TI related to the ß-globin gene only. Nevertheless, some of them displayed complications such as cholelithiasis or extramedullary hematopoiesis. In addition, one third of the cohort needed transfusions and another third was under iron chelation. CONCLUSION: The genotype associating a heterozygous ß0 or ß+ -thalassemia mutation with a triplication at HBA locus should be accurately diagnosed as it could lead to symptomatic anemia and to potential iron overload and iron-related complications even in patients with no transfusion need.

Tandem Triplication 11p15.5-ICR1 (H19/IGF2) Detected by Microarray and Optical Genome Mapping in a Prenatal Beckwith-Wiedemann Case.

Optical genome mapping (OGM) appears as a new tool for matching standard cytogenetic methods (karyotype and microarray) into a single assay. The chromosomal region 11p15.5 harbours two differentially methylated regions, the imprinting centre regions 1 and 2 (ICR1, ICR2). Disturbances in both regions alter human growth and are associated with two imprinting disorders, Beckwith-Wiedemann (BWS) and Silver-Russell syndromes. Herein, we present a prenatal case with a triplication in 11p15.5, including the H19/IGF2 imprinted region, detected by microarray and OGM. A 30-year-old pregnant woman of 17 weeks of gestation was referred for prenatal karyotype and microarray study because of increased nuchal translucency, short femur, megabladder, hyperechogenic bowel, and renal ectasia. Microarray, OGM, and MS-MLPA were performed, and a tandem cis-triplication in 11p15.5 and hypermethylation of the ICR1 region, compatible with BWS was detected. OGM, with its power to detect all classes of structural variants, including copy number variants, at a higher resolution than traditional cytogenetic methods can play a significant role in prenatal care and management as a next-generation cytogenomic tool. This study further supports the hypotheses that the amplification/duplication-triplication of the H19/IGF2 region could be related to BWS if it is of paternal origin.

Triplications of chromosome 1p36.3, including the genes GABRD and SKI, are associated with a developmental disorder and a facial gestalt.

Triplication of chromosomal region 1p36.3 is a rare genomic rearrangement. In this report, we delineate the phenotypic spectrum associated with 1p36.3 triplications. We describe four patients with microtriplications of variable size, but with a strong phenotypic overlap, and compare them to previously described patients with an isolated triplication or duplication of this region. The 1p36.3 triplication syndrome is associated with a distinct phenotype, characterized by global developmental delay, moderate intellectual disability, seizures, behavioral problems, and specific facial dysmorphic features, including ptosis, hypertelorism, and arched eyebrows. The de novo occurrence of these microtriplications demonstrates the reduced reproductive fitness associated with this genotype, in contrast to 1p36.3 duplications which are mostly inherited and can be associated with similar facial features but with a less severe developmental phenotype. The shared triplicated region encompasses four disease-related genes of which GABRD and SKI are most likely to contribute to the phenotype.

Triplication and tetraplication of the thumb: a modification of the Rotterdam classification.

We proposed a modification of the Rotterdam classification for thumb triplication and tetraplication. Twenty-one patients were included (24 cases of thumb triplication and four cases of tetraplication). These were analysed and classified according to a modification of the Rotterdam classification involving three steps; from the radial to ulnar side, we first identified each thumb on radiographs and gross appearance to divide into triplication or tetraplication. Second, we define the levels of duplication and established the nomenclature. Third, the aberrant features and their location were assigned for each thumb, again from radial to ulnar side. A surgical algorithm was also proposed. This modified classification may be helpful for characterizing the rare conditions of thumb triplication and tetraplication for use in patient and management and communication between surgeons.Level of evidence: III.

De novo triplication at 1p36.23p36.22 further refines the dosage sensitive region of overlap in Setleis syndrome (focal facial dermal dysplasia type III).

Setleis syndrome (SS), or focal facial dermal dysplasia type III (FFDD3, MIM #227260), is an autosomal recessive condition caused by biallelic loss-of-function variants in TWIST2. It is characterized by bitemporal atrophic skin lesions and distinctive facial features. Individuals with de novo or inherited duplication or triplication of the chromosomal region 1p36.22p36.21 have also been reported to have the SS phenotype with additional neurodevelopmental challenges (rarely seen in individuals with TWIST2 mutations) and variable expressivity and penetrance. Triplication of this region is also associated with more severe manifestations compared to a duplication. We report a 2-year-old female patient with features of SS associated with a de novo 3.603 Mb triplication at 1p36.23p36.22 identified on postnatal microarray analysis. Her triplication shares a 281.263 kb overlap with gains at 1p36.22, reported by previous groups, delineating the shortest region of overlap (SRO) to date. This SRO involves 10 RefSeq and 4 OMIM morbid map genes and highlights the candidate dosage-sensitive element(s) underlying the cardinal features of SS phenotype in individuals with gains at 1p36.