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Objective Methods Results Conclusion Rab11A is an important molecule for recycling endosomes and is closely related to the proliferation, invasion, and metastasis of tumors. This study investigated the prognostic and immune significance of Rab11A and validated its potential function and mechanism in breast cancer (BRCA).RNA sequencing data for 33 tumors were downloaded from The Cancer Genome Atlas (TCGA) and Genotype‐Tissue Expression databases. Correlation analysis was used to evaluate the relationship between Rab11A expression and immune characteristics. Potential pathways were identified using the Kyoto Encyclopedia of Genes and Genomes and Gene Ontology analysis. Immunohistochemical analysis, colony formation assay, bromodeoxyuridine incorporation assay, immunofluorescence, and Western blot were used to explore potential function and mechanism.Analysis of the TCGA database showed significant upregulation of Rab11A expression in a variety of cancers. Rab11A was up‐regulated in 82.4% of BRCA. High Rab11A expression is associated with poor survival in cancer patients and is a predictor of poor prognosis. CIBERSORT analysis showed that Rab11A was negatively associated with almost all immune cycle activity scores pan‐cancer. The results of the TCGA‐BRCA cohort were further confirmed by using pathological samples from clinical BRCA patients. The results showed that Rab11A expression was correlated with estrogen receptor (ER) and progesterone receptor expression in BRCA (p < 0.05). Knockdown and overexpression of Rab11A affected the proliferation of BRCA cells. Further mechanistic studies revealed that down‐regulation of ER alpha (ERα) and up‐regulation of ER beta (ERβ) mediated Rab11A‐induced inhibition of BRCA cell proliferation.Rab11A expression in pan‐cancer is associated with poor prognosis and immune profile. In particular, in BRCA, Rab11A expression regulates cell proliferation by targeting ERα and ERβ. High Rab11A expression is tightly associated with immune characteristics, tumor microenvironment, and genetic mutations. These results provide a reference for exploring the role of Rab11A in pan‐cancer and provide a new perspective for revealing potential therapeutic targets in BRCA. [ABSTRACT FROM AUTHOR]

The p53 mutation is the most common genetic mutation associated with human neoplasia. TP53 missense mutations, which frequently arise early in breast cancer, are present in over thirty percent of breast tumors. In breast cancer, p53 mutations are linked to a more aggressive course of the disease and worse overall survival rates. TP53 mutations are mostly seen in triple-negative breast cancer, a very diverse kind of the disease. The majority of TP53 mutations originate in the replacement of individual amino acids within the p53 protein's core domain, giving rise to a variety of variations referred to as "mutant p53s." In addition to gaining carcinogenic qualities through gain-of-function pathways, these mutants lose the typical tumor-suppressive features of p53 to variable degrees. The gain-of-function impact of stabilized mutant p53 causes tumor-specific dependency and resistance to therapy. P53 is a prospective target for cancer therapy because of its tumor-suppressive qualities and the numerous alterations that it experiences in tumors. Phenotypic abnormalities in breast cancer, notably poorly differentiated basal-like tumors are frequently linked to high-grade tumors. By comparing data from cell and animal models with clinical outcomes in breast cancer, this study investigates the molecular mechanisms that convert gene alterations into the pathogenic consequences of mutant p53's tumorigenic activity. The study delves into current and novel treatment approaches aimed at targeting p53 mutations, taking into account the similarities and differences in p53 regulatory mechanisms between mutant and wild-type forms, as well. [ABSTRACT FROM AUTHOR]

SUMMARY Ferns (Pteridophyta), as the second largest group of vascular plants, play important roles in ecosystem functioning. Homosporous ferns exhibit a remarkable range of mating systems, from extreme inbreeding to obligate outcrossing, which may have significant evolutionary and ecological implications. Despite their significance, the impact of genome‐wide inbreeding on genetic diversity and mutation load within the fern lineage remain largely unexplored. In this study, we utilized whole‐genome sequencing to investigate the genomic signatures of inbreeding and genetic load in three Alsophila tree fern species. Our analysis revealed extremely high inbreeding in A. spinulosa, in contrast to the predominantly outcrossing observed in A. costularis and A. latebrosa. This difference likely reflects divergent mating systems and demographic histories. Consistent with its extreme inbreeding propensity, A. spinulosa exhibits reduced genetic diversity and a pronounced decline in effective population size. Comparison of genetic load revealed an overall reduction in deleterious mutations in the highly inbred A. spinulosa, highlighting that long‐term inbreeding may have contributed to the purging of strongly deleterious mutations, thereby prolonging the survival of A. spinulosa. Despite this, however, A. spinulosa carries a substantive realized genetic load that may potentially instigate future fitness decline. Our findings illuminate the complex evolutionary interplay between inbreeding and mutation load in homosporous ferns, yielding insights with important implications for the conservation and management of these species. [ABSTRACT FROM AUTHOR]

Background and purpose Methods Results Conclusions Spinal muscular atrophy (SMA) is a genetic disorder caused by SMN1 gene mutations. Although studies on available disease‐modifying treatments have reported their efficacy and safety, long‐term natural history data are lacking for comparison. The aim of this prospective study was to report 4‐year changes on the Hammersmith Functional Motor Scale Expanded (HFMSE) in type II and III SMA in relation to several variables such as age, functional status and SMN2 copy number.The study involves retrospective analysis of prospectively collected data from international datasets (Belgium, Italy, Spain, USA, UK). HFMSE longitudinal changes were analyzed using linear mixed effect models, examining annualized HFMSE change and its association with variables such as age at baseline, sex, motor function, SMN2 copy number.In SMA type II (n = 226), the 4‐year mean change was −2.20 points. The largest mean changes were observed in sitters aged 5–14 years and the lowest in those who lost the ability to sit unsupported. In SMA type III (n = 162), the 4‐year mean change was −2.75 points. The largest mean changes were in those aged 7–15 years, whilst the lowest were in those below 7 and in the SMA type IIIa subgroup over 15. Age and score at baseline were predictive of 4‐year changes.Our findings provide natural history reference data for comparison with long‐term follow‐up of clinical trials or real‐world data, highlighting the need to define patterns of changes in smaller SMA subgroups instead of reporting mean changes across an entire SMA cohort. [ABSTRACT FROM AUTHOR]

Background: Accurate and robust drug response prediction is of utmost importance in precision medicine. Although many models have been developed to utilize the representations of drugs and cancer cell lines for predicting cancer drug responses (CDR), their performances can be improved by addressing issues such as insufficient data modality, suboptimal fusion algorithms, and poor generalizability for novel drugs or cell lines. Results: We introduce TransCDR, which uses transfer learning to learn drug representations and fuses multi-modality features of drugs and cell lines by a self-attention mechanism, to predict the IC50 values or sensitive states of drugs on cell lines. We are the first to systematically evaluate the generalization of the CDR prediction model to novel (i.e., never-before-seen) compound scaffolds and cell line clusters. TransCDR shows better generalizability than 8 state-of-the-art models. TransCDR outperforms its 5 variants that train drug encoders (i.e., RNN and AttentiveFP) from scratch under various scenarios. The most critical contributors among multiple drug notations and omics profiles are Extended Connectivity Fingerprint and genetic mutation. Additionally, the attention-based fusion module further enhances the predictive performance of TransCDR. TransCDR, trained on the GDSC dataset, demonstrates strong predictive performance on the external testing set CCLE. It is also utilized to predict missing CDRs on GDSC. Moreover, we investigate the biological mechanisms underlying drug response by classifying 7675 patients from TCGA into drug-sensitive or drug-resistant groups, followed by a Gene Set Enrichment Analysis. Conclusions: TransCDR emerges as a potent tool with significant potential in drug response prediction. [ABSTRACT FROM AUTHOR]

Azithromycin, a macrolide antibioticum, is the first‐line treatment for Mycoplasma genitalium (MG), but resistant MG is an increasing problem. Macrolide resistance‐mediated mutations (MRM) has been linked to point mutations in region V of the MG 23S rRNA gene. We have evaluated an open access analyzer (Panther Fusion, Hologic Inc) for detectability of MRM (mutations A2071G and A2072G) and MG wild type (WT) in clinical samples. Also, the agreement of the Panther Fusion assay results with a corresponding established In‐house MRM‐WT PCR (ABI 7500) was calculated. Left over material from 55 clinical samples positive for MG by the Aptima test (Hologic) based on transcription‐mediated amplification (TMA), collected from January to February 2023 in Region Skåne, Sweden, was analyzed. Specific amplification curves were generated for positive controls of MG mutations (A2071G and A2072G) and WT by the Panther Fusion assay. The limit of detection (LOD) was 5.3 copies/mL for WT, 8.1 copies/mL for mutation A2071G, and 81 copies/mL for mutation A2072G. The overall concordance was 91% between the Panther Fusion and the In‐house PCR (Kappa 0.621, 95% CI; 0.327–0.914) for detection of WT or MRM in MG‐positive clinical samples. The Panther Fusion detected MRM in 20% (11/55) and WT in 62% (34/55) of the samples. The corresponding In‐house PCR results were 25% (14/55) and 65% (36/55). In summary, the Panther Fusion assay demonstrated detection of low copy number of MRM and WT of MG. Among clinical samples substantial agreement between the Panther Fusion and In‐house PCR results was observed. Integrating MG‐analysis (TMA) and MRM‐WT assay on the Panther platform could make MRM testing more readily available. However, the Panther Fusion had a lower success rate (82% vs 90%) for macrolide susceptibility testing, hence testing with a complementary method should be considered for samples where neither WT nor MRM MG are detectable. [ABSTRACT FROM AUTHOR]

Background: Error-corrected next-generation sequencing (ecNGS) technologies have enabled the direct evaluation of genome-wide mutations after exposure to mutagens. Previously, we reported an ecNGS methodology, Hawk-Seq™, and demonstrated its utility in evaluating mutagenicity. The evaluation of technical transferability is essential to further evaluate the reliability of ecNGS-based assays. However, cutting-edge sequencing platforms are continually evolving, which can affect the sensitivity of ecNGS. Therefore, the effect of differences in sequencing instruments on mutation data quality should be evaluated. Results: We assessed the performance of four sequencing platforms (HiSeq2500, NovaSeq6000, NextSeq2000, and DNBSEQ-G400) with the Hawk-Seq™ protocol for mutagenicity evaluation using DNA samples from mouse bone marrow exposed to benzo[a]pyrene (BP). The overall mutation (OM) frequencies per 106 bp in vehicle-treated samples were 0.22, 0.36, 0.46, and 0.26 for HiSeq2500, NovaSeq6000, NextSeq2000, and DNBSEQ-G400, respectively. The OM frequency of NextSeq2000 was significantly higher than that of HiSeq2500, suggesting the difference to be based on the platform. The relatively higher value in NextSeq2000 was a consequence of the G:C to C:G mutations in NextSeq2000 data (0.67 per 106 G:C bp), which was higher than the mean of the four platforms by a ca. of 0.25 per 106 G:C bp. A clear dose-dependent increase in G:C to T:A mutation frequencies was observed in all four sequencing platforms after BP exposure. The cosine similarity values of the 96-dimensional trinucleotide mutation patterns between HiSeq and the three other platforms were 0.93, 0.95, and 0.92 for NovaSeq, NextSeq, and DNBSeq, respectively. These results suggest that all platforms can provide equivalent data that reflect the characteristics of the mutagens. Conclusions: All platforms sensitively detected mutagen-induced mutations using the Hawk-Seq™ analysis. The substitution types and frequencies of the background errors differed depending on the platform. The effects of sequencing platforms on mutagenicity evaluation should be assessed before experimentation. [ABSTRACT FROM AUTHOR]

The incidence of multiple primary lung cancer (MPLC) is increasing, with some of our surgical patients exhibiting numerous lesions. We defined lung cancer with five or more primary lesions as super MPLCs. Elucidating the genomic characteristics of this special MPLC subtype can help reduce disease burden and understand tumor evolution. In our cohort of synchronous super early-stage MPLCs (PUMCH-ssesMPLC), whole-exome sequencing on 130 resected malignant specimens from 18 patients provided comprehensive super-MPLC genomic landscapes. Mutations are enriched in PI3k-Akt and MAPK pathways. Their BRAF mutation frequency (31.5%) is significantly higher than MPLC with fewer lesions and early-stage single-lesion cancer, while EGFR mutations are significantly fewer (13.8%). As lesion counts increase, BRAF mutations gradually become dominant. Also, invasive lesions more tend to have classic super-MPLC mutation patterns. High-frequency BRAF mutations, especially Class II, and low-frequency EGFR mutations could be a reason for the limited effectiveness of targeted therapy in super-MPLC patients. [ABSTRACT FROM AUTHOR]

Tigecycline (TGC) is currently used to treat carbapenem-resistant Acinetobacter baumannii (CRAB) infections, while eravacycline (ERV), a new-generation tetracycline, holds promise as a novel therapeutic option for these infections. However, differences in resistance mechanism between ERV and TGC against A. baumannii remain unclear. This study sought to compare the characteristics and mechanisms of ERV and TGC resistance among clinical A. baumannii isolates. A total of 492 isolates, including 253 CRAB and 239 carbapenemsensitive A. baumannii (CSAB) isolates, were collected from hospitalized patients in China. The MICs of ERV and TGC against A. baumannii were determined by broth microdilution. Genetic mutations and expressions of adeB, adeG, adeJ, adeS, adeL, and adeN in resistant strains were examined by PCR and qPCR, respectively. The in vitro recombination experiments were used to verify the resistance mechanism of ERV and TGC in A. baumannii. The MIC90 of ERV in CRAB and CSAB isolates were lower than those of TGC. A total of 24 strains resistant to ERV and/or TGC were categorized into three groups: only ERVresistant (n = 2), both ERV- and TGC-resistant (n = 7), and only TGC-resistant (n = 15). ST208 (75%, n = 18) was a major clone that has disseminated in all three groups. The ISAba1 insertion in adeS was identified in 66.7% (6/9) of strains in the only ERV-resistant and both ERV- and TGC-resistant groups, while the ISAba1 insertion in adeN was found in 53.3% (8/15) of strains in the only TGC-resistant group. The adeABC and adeRS expressions were significantly increased in the only ERV-resistant and both ERV- and TGC-resistant groups, while the adeABC and adeIJK expressions were significantly increased and adeN was significantly decreased in the only TGC-resistant group. Expression of adeS with the ISAba1 insertion in ERV- and TGC-sensitive strains significantly increased the ERV and TGC MICs and upregulated adeABC and adeRS expressions. Complementation of the wildtype adeN in TGC-resistant strains with the ISAba1 insertion in adeN restored TGC sensitivity and significantly downregulated adeIJK expression. In conclusion, our data illustrates that ERV is more effective against A. baumannii clinical isolates than TGC. ERV resistance is correlated with the ISAba1 insertion in adeS, while TGC resistance is associated with the ISAba1 insertion in adeN or adeS in A. baumannii. [ABSTRACT FROM AUTHOR]

SARS-CoV-2 JN.1 with an additional L455S mutation on spike when compared with its parental variant BA.2.86 has outcompeted all earlier variants to become the dominant circulating variant. Recent studies investigated the immune resistance of SARS-CoV-2 JN.1 but additional factors are speculated to contribute to its global dominance, which remain elusive until today. Here, we find that SARS-CoV-2 JN.1 has a higher infectivity than BA.2.86 in differentiated primary human nasal epithelial cells (hNECs). Mechanistically, we demonstrate that the gained infectivity of SARS-CoV-2 JN.1 over BA.2.86 associates with increased entry efficiency conferred by L455S and better spike cleavage in hNECs. Structurally, S455 altered the mode of binding of JN.1 spike protein to ACE2 when compared to BA.2.86 spike at ACE2H34, and modified the internal structure of JN.1 spike protein by increasing the number of hydrogen bonds with neighboring residues. These findings indicate that a single mutation (L455S) enhances virus entry in hNECs and increases immune evasiveness, which contribute to the robust transmissibility of SARS-CoV-2 JN.1. We further evaluate the in vitro and in vivo virological characteristics between SARS-CoV-2 BA.2.86/JN.1 and EG.5.1/HK.3, and identify key lineage-specific features of the two Omicron sublineages that contribute to our understanding on Omicron antigenicity, transmissibility, and pathogenicity. Here, the authors show that a single mutation in JN.1 spike, L455S, confers better spike cleavage and enhances virus infectivity in differentiated primary human nasal epithelial cells while increasing immune evasiveness, contributing to the efficient spread of JN.1. [ABSTRACT FROM AUTHOR]

Background: Adenomatous polyposis coli (APC) gene, an oncogene, has been implicated in stomach adenocarcinoma (STAD), which is a common type of gastric cancer (GC). Although the relationship between APC gene mutations and gastric adenocarcinoma has been comprehensively studied, the potential role of these mutations in the prognosis and targeted therapy remains known. Methods: We utilized The Cancer Genome Atlas (TCGA) database to obtain gene expression matrices, clinical information, and mutation data from patients with STAD. The mutation status of the APC gene was analyzed, and its correlation with tumor mutational burden (TMB), microsatellite instability (MSI), and clinical prognosis in STAD was investigated. Gene set enrichment analysis (GSEA) was conducted to explore the pathological role of APC gene mutations in STAD metabolic pathways. Drug sensitivity analysis was conducted to identify potential targeted antitumor drugs for patients with APC gene mutations in gastric adenocarcinoma. Results: The results revealed that 88% (46/52) of STAD samples had nonsynonymous mutations. The mutation group exhibited a significantly higher TMB than the wild‐type group (p < 0.001), and the percentage of high MSI (MSI‐H) was significantly higher in the mutation group than in the wild‐type group (p < 0.001). Patients with APC mutations had a worse prognosis than those with APC wild‐type (p = 0.009). The APC gene mutation group displayed significant enrichment in amino acids, RNA, and several pathways (|NES| > 1 and nominal p value < 0.01). Compared to the wild‐type group, the mutation group exhibited a higher infiltration proportion of natural killer (NK) cells resting and eosinophils, whereas a lower infiltration proportion of monocytes and resting mast cells (p value < 0.05). AZD5991 exhibited significant sensitivity in patients with STAD carrying APC mutations (p = 0.028). Conclusion:APC gene mutations play a crucial role in the prognosis, molecular characteristics, and potential therapeutic strategies for gastric adenocarcinoma. [ABSTRACT FROM AUTHOR]

ABSTRACT Empty follicle syndrome (EFS) is a disorder characterised by the unsuccessful retrieval of oocytes from matured follicles following ovarian stimulation for in vitro fertilisation (IVF). Genetic factors significantly contribute to this pathology. To date, an increasing number of genetic mutations associated with GEFS have been documented, however, some cases still remain unexplained by these previously reported mutations. Here, we identified a novel homozygous missense ZP1 variant (c.1096 C > T, p.Arg366Trp) in a female patient with GEFS from a consanguineous family who failed to retrieve any oocytes during two cycles of IVF treatment. We conducted a molecular dynamics simulation analysis on the mutant ZP1 model, revealing that the mutant ZP1 protein has an altered 3D structure, lower fluctuation, higher compactness and higher instability than wild‐type ZP1. Immunostaining, immunoblotting and co‐immunoprecipitation results showed that the homozygous missense mutation in ZP1 impaired protein secretion and weakened interactions between ZP1 and other ZP proteins, which may affect the ZP assembly. This study contributes to a more comprehensive understanding of the genetic aetiopathogenesis of GEFS. [ABSTRACT FROM AUTHOR]

Background: Glycogen storage disease type 5 (McArdle disease) leads to a deficiency in the activity of myophosphorylase resulting in an impaired glucose utilization. The disease can be caused by a variety of mutations in the PYGM gene, and its typical clinical manifestation is muscles weakness within the first three decades of life. Case presentation: In this case report we present the diagnostic work-up of a physically active 78-year-old Caucasian patient suffering from a 2-year history of progressive camptocormia including clinical, radiologic, histological, and genetic tests. There was no history of neuro-muscular diseases in the family. Serum CK levels were moderately increased while other blood/urine parameters were normal. Magnetic resonance imaging showed fatty remodeling of the muscles of the back. Histochemical examination of a muscle biopsy revealed the absence of myophosphorylase activity, while gene analysis identified a known early-onset McArdle mutation in the PYGM gene. Conclusion: This case highlights that the clinical spectrum of PYGM gene mutation typically manifest during adolescence, but it is also a differential diagnosis in late onset muscle disorders and emphases the investigation of the role of ACE inhibitors in this disease. [ABSTRACT FROM AUTHOR]

This scientific report aims to investigate the genotype-phenotype correlations of retinal hemangioblastoma (RH) in von Hippel-Lindau (VHL) disease. The study included 77 patients with genetically confirmed VHL disease who visited an ophthalmology clinic for the evaluation of RH. The presence, location, and size of RH were evaluated, Patients were categorized into three groups based on variants: HIF-1α binding site missense (HM), non-HIF-1α binding site missense (nHM), and truncating (TR) mutations. Fifty-six patients (72.7%) had RH in either eye, and 24 had bilateral RH. Sixteen patients (20.8%) had juxtapapillary RH in either eye. Nine patients had RH ≥ 2.0 disc diameters in size. VHL c.208G>A variant was the most frequent single mutation. Compared with patients having nHM mutations (15 patients) in VHL gene, patients with HM mutations (33 patients) or TR mutations (26 patients) presented a greater number of eyes affected (p = 0.007 and 0.004, respectively), a greater number of RH (p = 0.012 and 0.003, respectively), and more frequent presentation of large RH ≥ 2.0 disc diameters (p = 0.012, and 0.013, respectively). In conclusion, this study provides a deeper understanding of the genetic spectrum of VHL disease in Korean VHL disease and highlights the importance of the location of missense mutations regarding the risk of RH. [ABSTRACT FROM AUTHOR]

Acromelanism is a form of albinism observed in several vertebrate species. In mammals, acromelanism is known to be caused by mutations in the tyrosinase gene (TYR) that induce a temperature‐sensitive behavior of melanin synthesis, resulting in a characteristic hair color gradient. In birds, several phenotypes consistent with acromelanism have been reported, but their genetic basis remains unknown. This study aimed to identify the genetic basis of an acromelanistic phenotype in domesticated canaries known as pearl and test whether it is caused by the same molecular mechanism described for mammals. To do this, we compared the genomes of pearl and non‐pearl canaries and searched for potentially causative genetic mutations. Our results suggest that the pearl phenotype is caused by a mutation in the TYR gene encoding a TYR‐P45H missense substitution. Our findings further suggest that reports of acromelanism in other bird species might be explained by TYR mutations. [ABSTRACT FROM AUTHOR]

Background: Hepatic manifestations of hemophagocytic lymphohistiocytosis (HLH), an underrecognized primary presentation in pediatric age group, mandate high levels of suspicion for early diagnosis. Aim: This is to study the frequencies of clinical and laboratory hepatic involvement in patients with familial/primary or secondary/acquired HLH in relation to disease reactivation and outcome. Methods: A 6-month retrospective cohort study recruited 35 patients with HLH. Detailed clinical, laboratory, and genetic characteristics of HLH were collected. Hepatic transaminases and synthetic liver functions were collected at presentation, weeks 2 and 8 after starting treatment, and at time of reactivation. Biochemical liver involvement was considered when alanine aminotransferase (ALT) lived three-times more than the upper normal level. Overall (OS) and reactivation free survival were analyzed according to liver involvement. Results: Twenty patients (57%) had genetically confirmed HLH, 12 (34.3%) had MUNC13D mutations, 3 (8.5%) had STXBP2 mutations, and 5 (14.3%) had RAB27A mutations, while 9 (25.7%) had no genetic mutations with 4 of them had secondary HLH. Six patients (17.2%) patients had unknown genetics status. Median (IQR) age of the whole group was 18 months (6–36) with an age range of 2–108 months. Liver enlargement was detected at diagnosis in 29 (82.9%) and at reactivation in 18 (51.4%) patients. Eight (22.86%) patients had biochemical hepatic involvement at presentation with no significant difference in their demographic, initial clinical presentation, survival, or the type of mutant gene according to liver involvement. Conclusion: Variable hepatic biochemical involvement might be the presenting manifestation of HLH at diagnosis and upon reactivation, yet it did not impact disease outcome. [ABSTRACT FROM AUTHOR]

Predicting how new mutations alter phenotypes is difficult because mutational effects vary across genotypes and environments. Recently discovered global epistasis, in which the fitness effects of mutations scale with the fitness of the background genotype, can improve predictions, but how the environment modulates this scaling is unknown. We measured the fitness effects of ~100 insertion mutations in 42 strains of Saccharomyces cerevisiae in six laboratory environments and found that the global epistasis scaling is nearly invariant across environments. Instead, the environment tunes one global parameter, the background fitness at which most mutations switch sign. As a consequence, the distribution of mutational effects is predictable across genotypes and environments. Our results suggest that the effective dimensionality of genotype-to-phenotype maps across environments is surprisingly low. [ABSTRACT FROM AUTHOR]

BackgroundMethodsResultsDiscussionADAMTSL4-related eye disorder is a rare autosomal recessive disease with a wide spectrum of severity and expressivity. We describe the genotypic and phenotypic findings in a cohort of Ohio Anabaptist with a pathogenic ADAMTSL4 gene sequence variation.Patient phenotypes were gathered from clinical data. Genetic information was collected using clinical exome sequencing followed by Sanger sequencing.Five patients from three Ohio Anabaptist families were determined to have a homozygous recessive ADAMTSL4 20-bp (c.767_786del) sequence variant. All five patients were found to have varying degrees of ectopia lentis and three patients presented with symptomatic lens subluxation. Average age of ectopia lentis diagnosis was 5 years (range 2–7 years). Additional features included persistent pupillary membrane and pupillary margin irregularities. The remaining two patients were asymptomatic and were found to have mild lens subluxation in adulthood, as they were examined following family genetic testing. Twenty-six heterozygous carriers were identified in a database of 1426 Ohio Old Order Amish individuals with an estimated carrier frequency of ~1:54 (allele frequency 0.91%).This is the first study to identify an ADAMTSL4 gene mutation in the Anabaptist population. Despite sharing the same genetic mutation, patients presented with a wide range of manifestations. A portion of affected individuals likely remain undiagnosed in the Anabaptist and general populations, especially if they are asymptomatic and only have mild lens subluxation. Implementation of early genetic screenings in high-risk populations can lead to improved awareness and patient outcomes. [ABSTRACT FROM AUTHOR]

Background X-prolyl aminopeptidase 3: (XPNPEP3) mutations are known to cause nephronophthisis-like nephropathy-1 (NPHPL1), a rare autosomal-recessive kidney disease characterized by progressive kidney failure and cystic kidney disease in childhood. The full phenotypic spectrum associated with mutations in XPNPEP3 is not fully elucidated. Case presentation: A 13-year-old Chinese female patient with intellectual disability presented with a 2-year history of convulsions and fatigue, with a recent episode of swelling, breathlessness, and nocturnal dyspnea lasting 10 days. The patient was diagnosed with heart failure and kidney failure. Whole exome sequencing revealed a homozygous c.970–2 A > G mutation in XPNPEP3 associated with severe cardiac dysfunction and neurological symptoms, including epilepsy and intellectual disability. Notably, kidney ultrasound did not reveal the typical changes of NPHPL1, and kidney failure was hypothesized to be secondary to cardiac dysfunction rather than primary kidney pathology. Conclusions: This case suggests the possible association of additional phenotypic features associated with XPNPEP3 mutations, emphasizing the need for further investigation into the heterogeneous clinical presentations associated with XPNPEP3 mutations. The findings highlight the importance of considering alternative phenotypes in patients with genetic mutations traditionally associated with specific diseases. Segregation and functional analyses are necessary to determine causality between the c.970–2 A > G XPNPEP3 mutation and disease. [ABSTRACT FROM AUTHOR]

Hyperekplexia is a neurologic disorder characterized by an exaggerated startle reflex in response to different types of stimuli. Hyperekplexia is defined by the triad of neonatal hypertonia, excessive startle reflexes, and generalized stiffness following the startle. Although uncommon, hyperekplexia can lead to serious consequences such as falls, brain injury, or sudden infant death syndrome. Aim of this study was to identify cases of neonatal hyperekplexia with a confirmed genetic diagnosis and to establish the genotype-phenotype correlation at onset. Articles were selected from 1993 to 2024 and PRISMA Statement was applied including newborns within 28 days of life. So, we retrieved from literature 14 cases of genetically confirmed neonatal hyperekplexia. The onset of clinical manifestations occurred in the first day of life in 8 of 14 patients (57.14%). Clinical findings were muscle stiffness (100%), startle reflex (66.66%), apnea/cyanosis (41.66%), positive nose-tapping test (33.33%), jerks (33.33%), jitteriness (25%), and ictal blinking (25%). Genes involved were GLRA1 in 9 of 14 (64.28%), SLC6A5 in 2 of 14 (14.28%), GPHN in 1 of 14 (7.14%), and GLRB in 2 of 14 (14.28%). Patients showed heterozygous (66.66%) or homozygous (33.33%) status. In 7 of 14 cases (50%), the condition occurred in other family members. A genotype-phenotype correlation was not achievable. Timely diagnosis is crucial to improve the natural history of hyperekplexia avoiding/reducing possible major complications such as sudden infant death syndrome, brain injury, and serious falls. Early differentiation from epilepsy minimizes treatment cost and improves the quality of life of patients. [ABSTRACT FROM AUTHOR]

Objective: Identification of driver mutations in tumors is an extremely important task in oncology for the choice of treatment strategy and assessment of therapy efficacy. In many cases, especially in disease monitoring, there is a need to detect a small number of copies of the mutant allele against the background of excessive content of wild-type DNA. Methods: Genomic DNA was isolated from tumor tissue in paraffine blocks and amplified using polymerase-chain reaction (PCR) with blocking of wild-type DNA amplification via addition of locked-nucleic acid (LNA) oligonucleotides. Fluorescently labelled PCR-product enriched by IDH-mutant alleles was hybridized on a biochip with immobilized oligonucleotide probes which was able to determine 5 mutations in the IDH1 gene and 2 mutations in the IDH2 gene. Results and Discussion: The method was developed and tested on a collection of 26 samples of paraffinized tumor tissue (glioma, glioblastoma, chondrosarcoma). In three cases, R132C, R132L, and R132H mutations in the IDH1 gene were detected in tumor samples with low representation of the mutant allele. The limit of detection of mutant DNA was determined to be 0.1% in the wild-type DNA background. The advantages of the method are simultaneous analysis of multiple targets, simplicity, reliability, and cost-effectiveness. Conclusions: A highly sensitive method for detecting somatic mutations in the IDH1/2 genes by LNA-mediated blocking of amplification of wild-type alleles and hybridization in a biological microchip was developed. We believe that the method may be useful for detecting low-abundance mutations in tumor samples, as well as in circular tumor DNA. [ABSTRACT FROM AUTHOR]

Hereditary tyrosinemia type 1 is an autosomal recessive disorder caused by mutations (pathogenic variants) in fumarylacetoacetate hydrolase, an enzyme involved in tyrosine degradation. Its loss results in the accumulation of toxic metabolites that mainly affect the liver and kidneys and can lead to severe liver disease and liver cancer. Tyrosinemia type 1 has a global prevalence of approximately 1 in 100,000 births but can reach up to 1 in 1,500 births in some regions of Québec, Canada. Mutating functionally related "modifier' genes (i.e. genes that, when mutated, affect the phenotypic impacts of mutations in other genes) is an emerging strategy for treating human genetic diseases. In vivo somatic genome editing in animal models of these diseases is a powerful means to identify modifier genes and fuel treatment development. In this study, we demonstrate that mutating additional enzymes in the tyrosine catabolic pathway through liver-specific genome editing can relieve or worsen the phenotypic severity of a murine model of tyrosinemia type 1. Neonatal gene delivery using recombinant adeno-associated viral vectors expressing Staphylococcus aureus Cas9 under the control of a liver-specific promoter led to efficient gene disruption and metabolic rewiring of the pathway, with systemic effects that were distinct from the phenotypes observed in whole-body knockout models. Our work illustrates the value of using in vivo genome editing in model organisms to study the direct effects of combining pathological mutations with modifier gene mutations in isogenic settings. [ABSTRACT FROM AUTHOR]

The distribution of fitness effects of new mutations plays a central role in evolutionary biology. Estimates of the distribution of fitness effect from experimental mutation accumulation lines are compromised by the complete linkage disequilibrium between mutations in different lines. To reduce the linkage disequilibrium, we constructed 2 sets of recombinant inbred lines from a cross of 2 Caenorhabditis elegans mutation accumulation lines. One set of lines ("RIAILs") was intercrossed for 10 generations prior to 10 generations of selfing; the second set of lines ("RILs") omitted the intercrossing. Residual linkage disequilibrium in the RIAILs is much less than in the RILs, which affects the inferred distribution of fitness effect when the sets of lines are analyzed separately. The best-fit model estimated from all lines (RIAILs + RILs) infers a large fraction of mutations with positive effects (∼40%); models that constrain mutations to have negative effects fit much worse. The conclusion is the same using only the RILs. For the RIAILs, however, models that constrain mutations to have negative effects fit nearly as well as models that allow positive effects. When mutations in high linkage disequilibrium are pooled into haplotypes, the inferred distribution of fitness effect becomes increasingly negative-skewed and leptokurtic. We conclude that the conventional wisdom—most mutations have effects near 0, a handful of mutations have effects that are substantially negative, and mutations with positive effects are very rare—is likely correct, and that unless it can be shown otherwise, estimates of the distribution of fitness effect that infer a substantial fraction of mutations with positive effects are likely confounded by linkage disequilibrium. [ABSTRACT FROM AUTHOR]

Hybrid male sterility is one of the fastest evolving intrinsic reproductive barriers between recently isolated populations. A leading explanation for the evolution of hybrid male sterility involves genomic conflicts with meiotic drivers in the male germline. There are, however, few examples directly linking meiotic drive to hybrid sterility. In this study, we report that the Sex-Ratio chromosome of Drosophila pseudoobscura , which causes X-chromosome drive within the USA subspecies, causes near-complete male sterility when it is moved into the genetic background of the Bogota subspecies. In addition, we show that this new form of sterility is genetically distinct from the sterility of F1 hybrid males in crosses between USA males and Bogota females. Our observations provide a tractable study system where noncryptic drive within species is transformed into strong hybrid sterility between very young subspecies. [ABSTRACT FROM AUTHOR]

Germline cells produce gametes, which are specialized cells essential for sexual reproduction. Germline cells first amplify through several rounds of mitosis before switching to the meiotic program, which requires specific sets of proteins for DNA recombination, chromosome pairing, and segregation. Surprisingly, we previously found that some proteins of the synaptonemal complex, a prophase I meiotic structure, are already expressed and required in the mitotic region of Drosophila females. Here, to assess if additional meiotic genes were expressed earlier than expected, we isolated mitotic and meiotic cell populations to compare their RNA content. Our transcriptomic analysis reveals that all known meiosis I genes are already expressed in the mitotic region; however, only some of them are translated. As a case study, we focused on mei-W68 , the Drosophila homolog of Spo11 , to assess its expression at both the mRNA and protein levels and used different mutant alleles to assay for a premeiotic function. We could not detect any functional role for Mei-W68 during homologous chromosome pairing in dividing germ cells. Our study paves the way for further functional analysis of meiotic genes expressed in the mitotic region. [ABSTRACT FROM AUTHOR]

Arginine–glycine–glycine motif proteins play a crucial role in determining mRNA fate. Suppressor of clathrin deficiency 6 (Scd6) is a conserved arginine–glycine–glycine motif containing ribonucleoprotein (RNP) condensate–resident, translation repressor, and decapping activator protein in Saccharomyces cerevisiae. Identifying protein factors that can modulate Scd6 function is critical to understanding the regulation of mRNA fate by Scd6. In this study, using an approach that combined mRNA tethering assay with flow cytometry, we screened 50 genes for their role in modulating the translation repression activity of Scd6. We identified 8 conserved modulators with human homologs. Of these, we further characterized in detail guanine nucleotide exchange factor Rho1 multicopy suppressor 2 (Rom2) and glycolytic enzyme triose phosphate dehydrogenase 3 (Tdh3), which, respectively, impede and promote translation repression activity of Scd6. Our study reveals that Rom2 negatively regulates the arginine methylation of Scd6 and antagonizes its localization to P-bodies. Tdh3 , on the other hand, promotes Scd6 interaction with Hmt1 , thereby promoting the arginine methylation of Scd6 and enhanced eIF4G1 interaction, which is known to promote its repression activity. Identifying these novel modulators provides exciting new insights into the role of a metabolic enzyme of the glycolytic pathway and guanine nucleotide exchange factor implicated in the cell wall integrity pathway in regulating Scd6 function and, thereby, cytoplasmic mRNA fate. [ABSTRACT FROM AUTHOR]

Neurons are highly polarized cells with dendrites and axons. Dendrites, which receive sensory information or input from other neurons, often display elaborately branched morphologies. While mechanisms that promote dendrite branching have been widely studied, less is known about the mechanisms that restrict branching. Using the nematode Caenorhabditis elegans , we identify rabr-1 (for Rab - related gene 1) as a factor that restricts branching of the elaborately branched dendritic trees of PVD and FLP somatosensory neurons. Animals mutant for rabr-1 show excessively branched dendrites throughout development and into adulthood in areas where the dendrites overlay epidermal tissues. Phylogenetic analyses show that RABR-1 displays similarity to small GTPases of the Rab - type, although based on sequence alone, no clear vertebrate ortholog of RABR-1 can be identified. We find that rabr-1 is expressed and can function in epidermal tissues, suggesting that rabr-1 restricts dendritic branching cell-nonautonomously. Genetic experiments further indicate that for the formation of ectopic branches rabr-1 mutants require the genes of the Menorin pathway, which have been previously shown to mediate dendrite morphogenesis of somatosensory neurons. A translational reporter for RABR-1 reveals a subcellular localization to punctate, perinuclear structures, which correlates with endosomal and autophagosomal markers, but anticorrelates with lysosomal markers suggesting an amphisomal character. Point mutations in rabr-1 analogous to key residues of small GTPases suggest that rabr-1 functions in a GTP-bound form independently of GTPase activity. Taken together, rabr-1 encodes for an atypical small GTPase of the Rab - type that cell-nonautonomously restricts dendritic branching of somatosensory neurons, likely independently of GTPase activity. [ABSTRACT FROM AUTHOR]

Shc (Src homologous and collagen) proteins function in many different signaling pathways where they mediate phosphorylation-dependent protein–protein interactions. These proteins are characterized by the presence of two phosphotyrosine-binding domains, an N-terminal PTB and a C-terminal SH2. We describe a previously unrecognized Caenorhabditis elegans Shc gene, shc-3 and characterize its role in stress response. Both shc-3 and shc-1 are required for long-term survival in L1 arrest and survival in heat stress, however, they do not act redundantly but rather play distinct roles in these processes. Loss of shc-3 did not further decrease survival of daf-16 mutants in L1 arrest, suggesting that like SHC-1, SHC-3 functions in the insulin-like signaling pathway. In the absence of SHC-3, DAF-16 nuclear entry and exit are slowed, suggesting that SHC-3 is required for rapid changes in DAF-16 signaling. [ABSTRACT FROM AUTHOR]

The article focuses on the molecular analysis of two-and-a-half-year-old twins diagnosed with odontohypophosphatasia due to a missense mutation in the alkaline phosphatase biomineralization associated (ALPL) gene. Topics discussed include the clinical presentation and diagnosis, identification of a novel heterozygous missense mutation (c.224G>A) in ALPL, and its predicted impact on tissue-nonspecific alkaline phosphatase (TNSALP) function.

Objectives: Ameloblastoma (AM), a locally aggressive tumor with extensive growth capacity, causes significant damage to the jaw and affects facial appearance. Although the high prevalence of BRAF V600E mutation in AM is known, its specific impacts on patients with AM remain unclear. Thus, the present study investigated the role of BRAF V600E mutation, thereby focusing on its impact on AM invasion and growth. Materials and Methods: Immunohistochemical analysis was used to compare BRAF V600E, MMP2, MMP9, and Ki‐67 expressions in AM (n = 49), normal oral mucosa (NOM) (n = 10), and odontogenic keratocyst (OKC) (n = 15) tissues. AM was further classified according to the presence or absence of BRAF V600E. The relationship between BRAF V600E and invasion as well as growth was evaluated. In addition, correlation analysis was performed using immunohistochemistry and confirmed via double‐labeling immunofluorescence. Finally, comparative analyses using mass spectrometry, immunohistochemistry, and immunofluorescence were performed to explore and identify underlying mechanisms. Results: AM exhibited a higher incidence of BRAF V600E mutation than NOM and OKC. BRAF V600E expression was positively correlated with the invasion‐associated proteins MMP2 and MMP9 and the growth‐related protein Ki‐67. Proteomic data revealed that BRAF V600E primarily activates the MAPK signaling pathway in AM, particularly driving the phosphorylation of extracellular signal‐regulated kinase 1/2 (ERK1/2). Conclusions: In summary, the findings suggested that the BRAF V600E mutation enhances the invasion and growth abilities of AM via the MAPK/ERK signaling pathway. Thus, targeting BRAF V600E or the MAPK/ERK pathway may be a potential AM therapy. [ABSTRACT FROM AUTHOR]

Objective: Tooth agenesis is a common craniofacial malformation, which is often associated with gene mutations. The purpose of this research was to investigate and uncover ectodysplasin A (EDA) gene variants in eight Chinese families affected with tooth agenesis. Methods: Genomic DNA was extracted from tooth agenesis families and sequenced using whole‐exome sequencing. The expression of ectodysplasin A1 (EDA1) protein was studied by western blot, binding activity with receptor was tested by pull‐down and the NF‐κB transcriptional activity was analyzed by Dual luciferase assay. Results: Eight EDA missense variants were discovered, of which two (c.T812C, c.A1073G) were novel. The bioinformatics analysis indicated that these variants might be pathogenic. The tertiary structure analysis revealed that these eight variants could cause structural damage to EDA proteins. In vitro functional studies demonstrated that the variants greatly affect protein stability or impair the EDA‐EDAR interaction; thereby significantly affecting the downstream NF‐κb transcriptional activity. In addition, we summarized the genotype–phenotype correlation caused by EDA variants and found that EDA mutations leading to NSTA are mostly missense mutations located in the TNF domain. Conclusion: Our results broaden the variant spectrum of the EDA gene associated with tooth agenesis and provide valuable information for future genetic counseling. [ABSTRACT FROM AUTHOR]

Objective: To investigate the genetic causes of 22 patients with clinically high suspicion of X‐linked hypohidrotic ectodermal dysplasia from 20 unrelated Chinese families, expand the spectrum of ectodysplasin‐A mutations, and provide more evidence for variants of uncertain significance. Subjects and Methods: Whole‐exome sequencing was performed and potentially pathogenic variants were verified by Sanger sequencing. Western blotting, real‐time PCR and immunofluorescence analyses were performed to investigate the preliminary functions of the candidate variants. Results: Nineteen ectodysplasin‐A variants were identified, six of which were not previously reported. Among these variants, we identified a patient who carried two mutations in ectodysplasin‐A and exhibited more severe phenotypes. Additionally, mutant protein expression levels decreased, whereas mRNA transcription levels increased. Cellular sublocalisation of the variants located in the tumour necrosis factor homologous domain showed that the proteins accumulated in the nucleus, whereas wild‐type proteins remained in the cell membrane. A rare indel variant and two classical splicing variants that lead to exon 7 skipping were detected. Conclusions: This study provides definitive diagnoses for 20 families with suspected X‐linked hypohidrotic ectodermal dysplasia and additional information on clinical heterogeneity and genotype–phenotype relationships. [ABSTRACT FROM AUTHOR]

Osteogenic differentiation of human bone marrow-derived mesenchymal stem cells (hBMSCs) is important for human bone formation. Long non-coding RNAs (lncRNAs) are critical regulators in osteogenic differentiation. This study aimed to explore the function and mechanisms of long intergenic non-protein coding RNA 963 (LINC00963) in affecting osteogenesis. Cell differentiation was assessed by alkaline phosphatase (ALP) activity detection and ALP staining assay. Meanwhile, levels of osteogenic marker genes, including RUNX family transcription factor 2 (RUNX2), osteocalcin (OCN), and osteopontin (OPN), were detected by RT-qPCR and western blot. Cell proliferation and apoptosis were measured using CCK-8 assay and flow cytometry analysis. RNA immunoprecipitation (RIP), RNA pull-down and luciferase reporter assays were used to investigate the interaction between genes. LINC00963 expression was down-regulated in hBMSCs treated with osteogenic induction. LINC00963 overexpression inhibited hBMSCs differentiation, proliferation, and elevated apoptosis. LINC00963 acted as a competing endogenous RNA (ceRNA) to interact with miR-10b-5p and thereby regulated the expression level of Ras-related protein Rap-2a (RAP2A). LINC00963 regulated RAP2A to inhibit the level of phosphorylated AKT (p-AKT). LINC00963 inhibited hBMSCs differentiation, proliferation, and elevated apoptosis via the miR-10b-5p/RAP2A/AKT signaling, which might help improve the treatment of osteoporosis. [ABSTRACT FROM AUTHOR]

Electroencephalogram (EEG) and electromyogram (EMG) are fundamental tools in sleep research. However, investigations into the statistical properties of rodent EEG/EMG signals in the sleep–wake cycle have been limited. The lack of standard criteria in defining sleep stages forces researchers to rely on human expertise to inspect EEG/EMG. The recent increasing demand for analysing large‐scale and long‐term data has been overwhelming the capabilities of human experts. In this study, we explored the statistical features of EEG signals in the sleep–wake cycle. We found that the normalized EEG power density profile changes its lower and higher frequency powers to a comparable degree in the opposite direction, pivoting around 20–30 Hz between the NREM sleep and the active brain state. We also found that REM sleep has a normalized EEG power density profile that overlaps with wakefulness and a characteristic reduction in the EMG signal. Based on these observations, we proposed three simple statistical features that could span a 3D space. Each sleep–wake stage formed a separate cluster close to a normal distribution in the 3D space. Notably, the suggested features are a natural extension of the conventional definition, making it useful for experts to intuitively interpret the EEG/EMG signal alterations caused by genetic mutations or experimental treatments. In addition, we developed an unsupervised automatic staging algorithm based on these features. The developed algorithm is a valuable tool for expediting the quantitative evaluation of EEG/EMG signals so that researchers can utilize the recent high‐throughput genetic or pharmacological methods for sleep research. [ABSTRACT FROM AUTHOR]

Aim: Endometriosis is a complex, multifactorial disease. Recent advances in molecular biology underscore that somatic mutations within the epithelial component of the normal endometrium, alongside aberrant epigenetic alterations within endometrial stromal cells, may serve as stimulators for the proliferation of endometriotic tissue within the peritoneal cavity. Nevertheless, pivotal inquiries persist: the deterministic factors driving endometriosis development in certain women while sparing others, notwithstanding comparable experiences of retrograde menstruation. Within this review, we endeavor to synopsize the current understanding of diverse pathophysiologic mechanisms underlying the initiation and progression of endometriosis and delineate avenues for future research. Methods: A literature search without time restriction was conducted utilizing PubMed and Google Scholar. Results: Given that aberrant clonal expansion stemming from cancer‐associated mutations is common in normal endometrial tissue, only endometrial cells harboring mutations imparting proliferative advantages may be selected for survival outside the uterus. Endometriotic cells capable of engendering metabolic plasticity and modulating mitochondrial dynamics, thereby orchestrating responses to hypoxia, oxidative stress, inflammation, hormonal stimuli, and immune surveillance, and adeptly acclimating to their harsh surroundings, stand a chance at viability. Conclusion: The genesis of endometriosis appears to reflect the evolutionary principles of mutation, selection, clonal expansion, and adaptation to the environment. [ABSTRACT FROM AUTHOR]

Homozygous familial hypercholesterolemia (HoFH), is a rare genetic disorder characterized by dual mutations in the low-density lipoprotein receptor (LDLR) gene, leading to dysfunctional or absent LDLRs, often accompanied by severe premature Atherosclerotic Cardiovascular Disease (ASCVD) and exhibiting refractoriness to aggressive pharmacological interventions. Double filtration plasmapheresis (DFPP), a form of lipoprotein apheresis (LA), has been effectively utilized as an adjunctive treatment modality to reduce serum LDL-C levels in refractory cases of HoFH. Here, we report a case of a 36-year-old female with HoFH who developed xanthomas on her limbs and waist at age 7. Despite maximum-tolerated doses of statins from age 32, combined with ezetimibe and evolocumab, her LDL-C levels remained critically elevated at 12–14 mmol/L. Her genetic testing confirmed a homozygous LDLR mutation. At 35 years old, she experienced exertional chest pain, and percutaneous coronary intervention revealed severe calcific left main stenosis, necessitating stent implantation. Subsequently, she initiated once every 1–2 months DFPP. Pre-DFPP, her LDL-C and total cholesterol (TC) levels were 13.82 ± 3.28 and 15.45 ± 0.78 mmol/L, respectively. Post-DFPP, her LDL-C and TC levels significantly decreased to 2.43 ± 0.33 mmol/L (81.76 ± 4.11% reduction) and 3.59 ± 0.41 mmol/L (76.76 ± 2.75% reduction), respectively. Lipoprotein (a) and triglycerides also decreased by 89.10 ± 1.39% and 42.29 ± 15.68%,respectively. Two years later, there was no progression of coronary artery disease, and her symptoms and xanthomas regressed significantly. Collectively, DFPP effectively reduces LDL-C levels in refractory cases of HoFH and contributes to delaying ASCVD progression, representing an efficacious adjunctive therapeutic modality. [ABSTRACT FROM AUTHOR]

Background: Third-generation sequencing (TGS) based on long-read technology has been gradually used in identifying thalassemia and hemoglobin (Hb) variants. The aim of the present study was to explore genotype varieties of thalassemia and Hb variants in Quanzhou region of Southeast China by TGS. Methods: Included in this study were 6,174 subjects with thalassemia traits from Quanzhou region of Southeast China. All of them underwent common thalassemia gene testing using the DNA reverse dot-blot hybridization technology. Subjects who were suspected as rare thalassemia carriers were further subjected to TGS to identify rare or novel α- and β-globin gene variants, and the results were verified by Sanger sequencing and/or gap PCR. Results: Of the 6,174 included subjects, 2,390 (38.71%) were identified as α- and β-globin gene mutation carriers, including 40 carrying rare or novel α- and β-thalassemia mutations. The αCD30(−GAG)α and Hb Lepore-Boston-Washington were first reported in Fujian province Southeast China. Moreover, the βCD15(TGG> TAG), βIVS−II−761, β0-Filipino(~ 45 kb deletion), and Hb Lepore-Quanzhou were first identified in the Chinese population. In addition, 35 cases of Hb variants were detected, the rare Hb variants of Hb Jilin and Hb Beijing were first reported in Fujian province of China. Among them, one case with compound αααanti3.7 and Hb G-Honolulu variants was identified in this study. Conclusion: Our findings may provide valuable data for enriching the spectrum of thalassemia and highlight the clinical application value of TGS-based α- and β-globin genetic testing. [ABSTRACT FROM AUTHOR]

Objective Vacuoles, E1 enzyme, X-linked, autoinflammatory, somatic (VEXAS) syndrome is a complex immune disorder consequence of somatic UBA1 variants. Most reported pathogenic UBA1 variants are missense or splice site mutations directly impairing the translational start site at p.Met41, with recent studies showing that these variants are frequent causes of recurrent inflammation in older individuals. Here we aimed to characterize a novel UBA1 variant found in two patients clinically presenting with VEXAS syndrome. Methods Patients' data were collected from direct assessments and from their medical charts. Genomics analyses were undertaken by both Sanger and amplicon-based deep sequencing, and mRNA studies were undertaken by both cDNA subcloning and mRNA sequencing. Results We report a novel, somatic variant in a canonical splice site of the UBA1 gene (c.346-2A>G), which was identified in two unrelated adult male patients with late-onset, unexplained inflammatory manifestations including recurrent fever, Sweet syndrome-like neutrophilic dermatosis, and lung inflammation responsive only to glucocorticoids. RNA analysis of the patients' samples indicated aberrant mRNA splicing leading to multiple in-frame transcripts, including a transcript retaining the full sequence of intron 4 and a different transcript with the deletion of the first 15 nucleotides of exon 5. Conclusion Here we describe abnormal UBA1 transcription as a consequence of the novel c.346-2A>G variant, identified in two patients with clinical features compatible with VEXAS syndrome. Overall, these results further demonstrate the expanding spectrum of variants in UBA1 leading to pathology and provide support for a complete gene evaluation in those patients considered candidates for VEXAS syndrome. [ABSTRACT FROM AUTHOR]

Objectives VEXAS syndrome is an autoinflammatory disease associated with a somatic mutation of the X-linked UBA1 gene in haematopoietic progenitor cells. This disorder was originally described as a disease affecting men, but rare cases of VEXAS syndrome in women have since been reported. The theoretical existence of phenotypic sex differences in this X-linked disease is debated. We compared the features of VEXAS syndrome between males and females to better understand this disorder and to improve its diagnostic accuracy in females. Methods From previously published clinical descriptions of VEXAS syndrome, we included studies that described patients with precise, individual VEXAS-related features. We formed a literature-based cohort of patients by collecting their clinical and biological data and compared the characteristics of male and female patients. Results We gathered 224 patient descriptions from 104 articles: 9 women and 215 men. Among the women, 1 had a constitutional 45,X karyotype and 4 had an acquired X monosomy in the bone marrow karyotype, while the marrow karyotype was not provided for the others. No difference was observed in the clinical or biological features according to sex. We also observed no difference in the type of UBA1 mutation or the association with myelodysplastic syndrome. Conclusions Our results supported the hypothesis that the UBA1 mutation should be sought under the same conditions in both sexes. As UBA1 is not subject to X-chromosome inactivation, VEXAS syndrome in females requires both UBA1 mutation and X monosomy, thus explaining the similarity between male and female VEXAS-related features and the lower prevalence of VEXAS syndrome in females. [ABSTRACT FROM AUTHOR]

Somatic mutations in genes encoding components of the RNA splicing machinery occur frequently in multiple forms of cancer. The most frequently mutated RNA splicing factors in cancer impact intronic branch site and 3′ splice site recognition. These include mutations in the core RNA splicing factor SF3B1 as well as mutations in the U2AF1/2 heterodimeric complex, which recruits the SF3b complex to the 3′ splice site. Additionally, mutations in splicing regulatory proteins SRSF2 and RBM10 are frequent in cancer, and there has been a recent suggestion that variant forms of small nuclear RNAs (snRNAs) may contribute to splicing dysregulation in cancer. Here, we describe molecular mechanisms by which mutations in these factors alter splice site recognition and how studies of this process have yielded new insights into cancer pathogenesis and the molecular regulation of splicing. We also discuss data linking mutant RNA splicing factors to RNA metabolism beyond splicing. Mutations in genes encoding components of the RNA splicing machinery occur frequently in multiple cancers. This review describes the molecular mechanisms by which cancer-associated mutations in splicing factors alter splice site recognition and how studies of this process have yielded new insights into cancer pathogenesis and the molecular regulation of splicing. [ABSTRACT FROM AUTHOR]

Background: Patients with programmed cell death‐ligand 1 (PD‐L1) ≥50% metastatic non‐small cell lung cancer (NSCLC) treated with first‐line immunotherapy showed heterogeneous tumor responses. In this study, we investigated the clinical and immune‐inflammatory markers distinguishing patients with metastatic NSCLC achieving high depth of tumor response (HDPR) from those with non‐high depth of response (NHDPR). The impact of clinical features on the prognosis of patients with PD‐L1 ≥50% were further clarified. Methods: The clinical characteristics and immune‐inflammatory markers of 17 patients with PD‐L1 ≥50% metastatic NSCLC at Beijing Tiantan Hospital between July 2020 and December 2023 were retrospectively analyzed. Results: Among the 17 patients, seven (41.2%) patients achieved HDPR (range: −50%, −72%) and 10 (58.8%) patients achieved NHDPR (range: −13%, −45%). Below normal CD4 + T lymphocytes/CD8 + T lymphocytes (CD4/CD8) ratio (p = 0.01) and oncogenes and/or tumor suppressor gene mutations (TP53/KRAS/EGFR) (p = 0.001) were found enriched for NHDPR compared with HDPR. With a median follow‐up of 26.0 months (range: 17.2–34.8 months), the median progression‐free survival (PFS) following first‐line immunotherapy and overall survival (OS) were 9.0 months (95% CI: 5.0–13.0) and not reached (NR), respectively. The neutrophil‐to‐lymphocyte ratio (NLR) was identified as an independent prognostic factor on first‐line PFS. Patients with an NLR ≥4 exhibited a shorter median PFS (7.0 months vs. NR; p = 0.033; 95% CI: 1.2–80.2) than those with an NLR <4 following first‐line immunotherapy. Conclusions: Among patients with PD‐L1 ≥50% metastatic NSCLC who received first‐line immunotherapy, a lower CD4/CD8 ratio and the presence of genes mutations showed a diminished tumor response and a higher NLR ratio exhibited a worse median PFS. [ABSTRACT FROM AUTHOR]

Background: Several computational and mathematical models of protein synthesis have been explored to accomplish the quantitative analysis of protein synthesis components and polysome structure. The effect of gene sequence (coding and non-coding region) in protein synthesis, mutation in gene sequence, and functional model of ribosome needs to be explored to investigate the relationship among protein synthesis components further. Ribosomal computing is implemented by imitating the functional property of protein synthesis. Result: In the proposed work, a general framework of ribosomal computing is demonstrated by developing a computational model to present the relationship between biological details of protein synthesis and computing principles. Here, mathematical abstractions are chosen carefully without probing into intricate chemical details of the micro-operations of protein synthesis for ease of understanding. This model demonstrates the cause and effect of ribosome stalling during protein synthesis and the relationship between functional protein and gene sequence. Moreover, it also reveals the computing nature of ribosome molecules and other protein synthesis components. The effect of gene mutation on protein synthesis is also explored in this model. Conclusion: The computational model for ribosomal computing is implemented in this work. The proposed model demonstrates the relationship among gene sequences and protein synthesis components. This model also helps to implement a simulation environment (a simulator) for generating protein chains from gene sequences and can spot the problem during protein synthesis. Thus, this simulator can identify a disease that can happen due to a protein synthesis problem and suggest precautions for it. [ABSTRACT FROM AUTHOR]

CADASIL is the most frequent hereditary cerebral small vessel disease worldwide. The disease is responsible for a slow and progressive accumulation of cerebral ischemic insults that lead to disabling cognitive and motor symptoms at late age. Although there is currently no cure for this condition, future therapies may concern subjects only at early stage of the disease. This will raise the question of the participation of asymptomatic carriers of pathogenic NOTCH3 gene mutation in future clinical trials, which will presuppose acceptance of presymptomatic genetic diagnosis. In this study, we questioned the population at risk of CADASIL who had not undergone a diagnostic procedure yet. Based on a questionnaire survey carried out by an independent team of sociologists, we analyzed what underlies the choice of people at risk to undergo or not to undergo a genetic test, and what could constitute the tipping point that could lead people who were initially not interested in their diagnosis to have recourse to it. Our results suggest that, far from being a simple, unequivocal path, the decision-making process leading to the choice of diagnosis is initially slowed down by the need to distance oneself from the disease so that it doesn't take over one's life, and then evolves under the influence of a complex tangle between advancing age, the presence of early symptoms, and the personal relationship with uncertainty. It cannot be ruled out that the real and imminent prospect of therapy may also modify responses to this type of survey. [ABSTRACT FROM AUTHOR]

Solid tumour tissue has traditionally been used for cancer molecular diagnostics. Recently, biomarker assessment in blood or liquid biopsies has become relevant because it allows genotyping in a less invasive and costly manner. In addition, it is a very useful technique in cases with insufficient tumour samples. Recent data have shown that this method can provide the baseline molecular characteristics of the tumour and resistance changes that emerge during cancer treatment. In terms of diagnostic application, the platforms available for clinical use in lung cancer focus on the isolation and detection of circulating DNA (ctDNA) and generally cover a limited number of mutations in genes such as epidermal growth factor receptor (EGFR), Kirsten rat sarcoma viral oncogene homolog (KRAS) and BRAF, as well as anaplastic lymphoma kinase (ALK) rearrangements. In parallel, there are plasma genotyping platforms based on next-generation sequencing (NGS) techniques, which are much broader in scope, allowing multiple genes to be studied simultaneously in a more efficient manner. More recently, promising research scenarios for liquid biopsy have emerged, such as its utility for early diagnosis and evaluation of minimal residual disease after oncological treatment. In light of these advances, knowledge of the benefits and limitations of liquid biopsy, as well as awareness of emerging information on new indications for this technique in non-small cell lung cancer (NSCLC), are of paramount importance in developing more effective management strategies for patients with this neoplasm. [ABSTRACT FROM AUTHOR]

Phosphate transporters in yeast cells are responsible for phosphorus homeostasis and are also indirectly involved in the regulation of various adaptive processes. One of these processes is the adaptation to ethanol consumption, which requires significant changes in phosphorus metabolism. We have demonstrated that knockout mutations in the genes PHO87, PHO89, PHO90, and PHO91, encoding phosphate transporters, impair the adaptation of Saccharomyces cerevisiae to ethanol consumption at an ethanol concentration of 4%. For these mutant strains, an extension of the lag phase and a decrease in the growth rate at the active stage were observed. Mutant cells differed from the parental strain in the content of inorganic polyphosphates, but not orthophosphate: they contained less long-chain polyphosphates when cultivated on ethanol, but not on glucose. When cultivated in a medium containing 4% ethanol, the strain with a knockout mutation in the PHO84 gene encoding the transporter of phosphate and divalent metals, as well as knockout strains for the PHM6 and PHM7 genes responsible for the polyphosphate overplus, did not show any growth differences compared to the parent strain in the medium with 4% ethanol. The possible role of phosphate transporters and inorganic polyphosphates in the adaptation of yeast to ethanol consumption is discussed. [ABSTRACT FROM AUTHOR]

Familial Mediterranean fever (FMF) is an autoinflammatory disease which may cause endothelial dysfunction and arterial stiffness. In this study, we evaluated patients with FMF in terms of arterial stiffness indicators and investigated whether there was any difference according to colchicine response. This is a single-center, prospective, case-control study conducted on pediatric patients with FMF. Patients were categorized into 2 groups: patients on colchicine monotherapy (group 1) and patients who used anti-interleukin-1 (IL-1) plus colchicine (group 2). Patient age, mutations in the MEFV gene, overall duration of treatments, and general characteristics of symptoms were recorded. Laboratory values in an attack-free period were noted. Pulse wave velocity (PWV) was measured in all patients. Erythrocyte sedimentation rate and C-reactive protein, nocturnal hypertension, and PWV were higher in group 2. Arterial stiffness develops due to subclinical inflammation in patients with FMF. It is more pronounced in colchicine-resistant patients. [ABSTRACT FROM AUTHOR]

The present study aimed at identifying the genetic mutation responsible for teratozoospermic infertility in a case with coiled sperm tails. A 33-year-old infertile male was diagnosed with teratozoospermic infertility, with sperm head in coiled (HIC) tail as the most common deformity. We employed whole exome sequencing to identify the genetic cause in this case. Exome sequencing data was filtered using the following criteria: MAF (< 0.003), ALFA project (< 0.001), 1000 Genomes (< 0.003), Granthem (> 50), Polyphen-2 (> 0.70), SIFT (< 0.03), and PhyloP (> = 0) scores. Shortlisted variants were looked in the in-house 29 exomes data available with us, and the variants that affected conserved amino acid residues or led to insertion/deletion or to protein-truncation with a Combined Annotation Dependent Depletion (CADD) score ≥ 10 were shortlisted. The variants thus populated were prioritized according to their roles in spermiogenesis. The study identified a heterozygous mutation c.826C > T (Arg276Trp) in the SPEM1 gene as a potential pathogenic variant that led to teratozoospermic infertility in the case under investigation. The mutation had a minor allele frequency of 0.00008176 in the gnomAd database and was absent in the Indian Genome Variations database. This is the first human study reporting a mutation in the SPEM1 gene as a cause of coiled sperm tails. [ABSTRACT FROM AUTHOR]

Currently, there is no robust evidence demonstrating a clear association between Lynch syndrome and non-malignant breast pathology such as adenomyoepithelioma. We report a case of benign breast adenomyoepithelioma, which after recurrence was associated with ductal carcinoma in-situ (DCIS) in a 41-year-old woman with Lynch syndrome, who lacked significant family history of breast or ovarian cancer. Both, the adenomyoepithelioma and DCIS were found to have nuclear loss of MSH2/MSH6 by immunohistochemistry, while germline testing confirmed MSH2 gene mutation. Concordant loss of MSH2 in both lesions in the context of a MSH2 pathogenic variant in this patient with Lynch syndrome illustrates that the benign adenomyoepithelioma behaved as a likely precursor of DCIS. Our report provides a novel perspective that in some patients with Lynch syndrome adenomyoepithelioma may represent a pre-malignant precursor lesion of DCIS. [ABSTRACT FROM AUTHOR]

Objectives: Observational studies have suggested an association between age at natural menopause (ANM) and ventricular structure and function. Nevertheless, the causal relationship remains unclear. This study aimed to evaluate the causal effects of ANM on ventricular structure and function by Mendelian randomization (MR) analysis. Methods: Genome-wide association summary statistics for ANM and 16 ventricular structures and functions were obtained. The inverse variance weighted (IVW) method was the primary MR approach for assessing causal associations. In addition, three additional MR methods (MR-Egger, weighted median and weighted mode) were performed to complement the IVW method. Furthermore, various sensitivity tests were conducted to evaluate the reliability of the MR results. Results: The IVW method identified no causal association between ANM and all 16 ventricular structures or functions (p > 0.05). Three additional MR methods yielded parallel results to the IVW approach (p > 0.05). Various sensitivity tests revealed stability of the MR results, indicating no heterogeneity or horizontal pleiotropy. Conclusion: The present MR study indicated that ANM would not causally affect ventricular structure or function. Therefore, the correlation between ANM and ventricular characteristics in previous observational studies might be attributed to shared upstream cardiovascular risk factors or unidentified genetic mutations that simultaneously affect both ANM and ventricular structure and function. [ABSTRACT FROM AUTHOR]

Context.--The distinction between well-differentiated epithelial favorable-histology Wilms tumor (EFHWT) and metanephric adenoma (MA) in children has historically been determined by the required absence of both a fibrous pseudocapsule and mitotic activity in MA. More recently these features have been allowed in adult MA. Mutations in exon 15 of the BRAF gene are reported in up to 88% of MAs but have not been reported in EFHWTs in children lacking MA features. Objective.--To clarify the pathologic and molecular features used to distinguish between pediatric MA and EFHWT. Design.--Stage I epithelial tumors classified as EFHWT on central review (36 patients) were identified from the Children's Oncology Group AREN03B2 study. Thirteen tumors had morphologic features overlapping those of MA and 23 lacked such features; 35 of 36 had tissue available for sequencing of BRAF. Results.--Patients with EFHWTs with MA features (13) were older (mean, 8.4 versus 1.9 years; P < .001), had smaller tumor diameters (mean, 6.0 versus 9.7 cm; P < .001), and had fewer mitoses (mean, 1 versus 48 mitoses per 10 high-power fields; P < .001) than patients with EFHWT lacking MA features (23). All EFHWTs with MA features contained at least a partial fibrous pseudocapsule; 7 of 12 (58%) had a BRAF exon 15 mutation. No BRAF exon 15 mutations were identified in 23 EFHWTs lacking MA features. None of the 13 EFHWT patients with MA features have experienced relapse (median follow-up 5.9 years). Conclusions.--Pediatric epithelial neoplasms with features of MA that show partial encapsulation and/or modest mitotic activity may be classified as MAs. Although BRAF mutation supports the diagnosis of MA, it is not required for the diagnosis. [ABSTRACT FROM AUTHOR]