Pathogenic Gene Research Articles

Exploring the pathophysiological mechanisms and wet biomarkers of VPS13A disease

VPS13A disease (also known as Chorea-Acanthocytosis, ChAc) is a representative subtype of the neuroacanthocytosis (NA) syndromes, characterized by neurodegeneration in the central nervous system and acanthocytosis in peripheral blood. It is a rare autosomal recessive genetic disorder caused by loss-of-function variants in the VPS13A gene, which is currently the only known pathogenic gene for ChAc. VPS13A protein is a member of novel bridge-like lipid transfer proteins family located at membrane contact sites, forming direct channels for lipid transport. The specific mechanism underlying how the loss of VPS13A function leads to the hematological and neurological phenotypes of the disease remains unclear. Here we present a review of recent studies on VPS13A protein and ChAc, focusing on the potential role of the VPS13A protein in pathophysiology of ChAc and also review the known and potential wet biomarkers of ChAc to enhance our comprehension of this rare disease.

Identification of stem melanosis of wheat (Pseudomonas cichorii) by real-time PCR

The phytopathogenic bacterium, Pseudomonas cichorii, affects a wide range of crops in filed and greenhouse production and causes wheat stem melanosis, which has been regulated by importers of Russian grain products. It is crucial to update the identification method based on real-time polymerase chain reaction (PCR) (PCR-RT). This method helps confirming P. cichorii in wheat samples. A 90 base pair long section of the hrcRST pathogenicity gene cluster was used as the target. Positive results were obtained for reference strains, confirmed by amplicon sequencing. Nucleotide sequences were then compared to the typical strain, DSM 50259. As a result of comparative DNA analysis, the sequences of the direct primer and probe were modified. The possibility of using a modification of 6FAM/BHQ1 dye/quencher available on the territory of the Russian Federation was demonstrated. The specificity of the new PCR-RT primer system PscF/PscHrc751R/PscP1 was assessed using 107 bacterial strains of the genus Pseudomonas, including P. cichorii, P. fuscovaginae, P. syringae, P. trivialis, P. viridiflava, P. chlororaphis, P. lutea and P. orientalis. The DNA of 4 strains (P. poae, P. graminis and 2 strains of P. fluorescens) showed a non-specific reaction at the 35–37 cycle threshold, with an accumulation that did not appear exponential. The analytical sensitivity of the test allows for the detection of P. cichorii at a concentration of 10^1 CFU/mL. The PCR-RV PscF/PscHrc751R/PscP1 test can be used as a screening tool for the detection of P. cichorii in plant products and for the characterization of pure bacterial cultures.

A case report of an individual with Creutzfeldt–Jakob disease characterized by prolonged isolated thalamic lesions and rare MM2-cortical-type pathology

BackgroundDiffusion-weighted magnetic resonance imaging (DWI) is essential for diagnosing Creutzfeldt–Jakob disease (CJD). Thalamic lesions are rarely detected by DWI in sporadic CJD (sCJD) cases with methionine homozygosity at polymorphic codon 129 (129MM) of the prion protein (PrP) gene. Here, we describe an unusual sCJD case, characterized by prolonged isolated thalamic diffusion hyperintensities and atypical brain pathology, in combination with the 129MM genotype.Case presentationA 72-year-old Japanese man developed a mild unsteady gait that had persisted for 1 year. DWI revealed isolated thalamic diffusion hyperintensities. Over the following 4 years, his condition progressed to include ataxia and cognitive decline. Repeated cerebrospinal fluid tests were negative for 14-3-3 protein, total tau protein, and real-time quaking-induced conversion assay. Electroencephalography did not show periodic sharp wave complexes or generalized periodic discharges. Despite these findings, thalamic DWI abnormalities persisted and evolved to include cortical lesions in the later stage of the disease. Genetic testing confirmed a 129MM genotype with no pathogenic PrP gene variants. Brain autopsy identified type 2 pathogenic PrP and the absence of the M2-thalamic prion strain, suggesting an MM2-cortical (MM2C)-subtype of sCJD. Histopathology revealed small vacuoles (sv) and patchy-perivacuolar PrP deposits without large vacuoles (lv). Patchy-perivacuolar deposits are a characteristic feature of the MM2C (lv) subtype and indicate MM2C (lv) pathology. Thus, this case was classified as a rare MM2C (sv + lv) subtype. No PrP protein staining was observed in the thalamus, despite spongiform changes with small vacuoles.ConclusionsThis case underscores the diagnostic challenges of atypical CJD with isolated thalamic abnormalities on DWI. Despite negative cerebrospinal fluid findings and clinical diagnostic criteria, persistent DWI abnormalities and evolving clinical symptoms continued to raise suspicion of CJD. A definitive diagnosis, being the MM2C (sv + lv) subtype of sCJD, was confirmed upon pathological examination. Even when atypical findings, such as isolated thalamic abnormalities, are observed and various tests are negative, if suspicion of CJD cannot be ruled out, it is important to confirm the diagnosis and pathological subtypes via postmortem analysis.

Identification of mutation of MYOC (c.1099G>A), a pedigree pathogenic gene of juvenile open angle glaucoma (JOAG): A case report

Rationale: The MYOC gene is associated with juvenile open-angle glaucoma (JOAG). This study aims to provide genetic counseling for a Chinese JOAG family by detecting MYOC mutations to identify high-risk individuals for early JOAG intervention. It also supplements the clinical characteristics of glaucoma patients with MYOC gene mutations. Patient concerns: A 43-year-old presented sought medical attention in a local hospital due to a 6-month decline in binocular vision. He was diagnosed as JOAG and underwent glaucoma surgery. The patient also had 11 family members with a history of JOAG. Diagnoses: After sequencing the polymerase chain reaction products of the patient, MYOC c.1099 G > A (p.G367R) mutation was observed. That is consistent with a diagnosis of JOAG. Intervention: Polymerase chain reaction analyses of 9 patients and 42 healthy family members were performed to explore potential mutations associated with familial JOAG. Outcomes: JOAG assisted in diagnosing the III-5 proband. Genetic detection indicated that III-5 was exposed to a novel heterozygous missense mutation of MYOC (c.1099 G > A [p.G367R]). The co-segregation of this gene with the trait observed in the pedigree was verified. All 10 participants exhibiting this mutation had JOAG phenotypes, whereas other participants did not show this mutation. In terms of MYOC mutation c.1099 G > A (p.G367R), this mutation occurred when the 1099th nucleotide in the encoding zone of MYOC changed from G to A. Moreover, the 367th amino acid coded by this base got mutated from glycine to arginine. DNAMAN sequence homology results showed that the G residues of MYOC: 367 were significantly conserved among different species. In addition, 3D protein conformation predicted that these mutations could decrease protein stability. Lessons: MYOC c.1099 G > A was identified as a pathogenic gene of JOAG in this pedigree. The addition of the MYOC mutant spectrum to JOAG in the Chinese population facilitates a complete understanding of the molecular pathogenesis and clinical diagnosis of MYOC.

MiR-PC-3p-241582_34 Contributes to the Infection of Athetis lepigone by Regulating the Expression of HSWP4 in Nosema bombycis.

Athetis lepigone is a recurring pest in the maize seedling stage under the wheat-maize no-tillage direct seeding system in China's summer maize region. Our previous research identified a highly pathogenic Nosema bombycis to A. lepigone, which spore wall protein plays an important role in the infection process. However, the regulatory mechanism of this spore wall protein is still unclear. In this study, we explored the regulatory mechanism of miRNAs on spore wall proteins. Transcriptome sequencing results showed that expression of the spore wall protein, HSWP4, significantly increased in the germination group compared to dormancy group. Silencing of HSWP4 reduced the number of microsporidian spores breaking through the midgut wall cells of A. lepigone. Association analysis of small RNA and mRNA revealed that the targeting site of miR-PC-3p-241582_34 on HSWP4 was located in the CDS region, and miR-PC-3p-241582_34 had a significant negative regulatory relationship with HSWP4. The dual luciferase reporter assay demonstrated that miR-PC-3p-241582_34 significantly affected the luciferase activity of the HSWP4-3'UTR expression vector (P < 0.05). Delivery of miRNA mimics decreased the expression of HSWP4 and inhibited the behavior of microsporidian spores breaking through the midgut wall of A. lepigone. On the other hand, delivery of inhibitors produced opposite results, indicating that the miR-HSWP4 pathway plays an important role in microsporidian infection of A. lepigone. This study provides a new theoretical basis for understanding the pathogenic mechanism and gene regulation of microsporidia, as well as for the green control of A. lepigone.

Disrupting the RNA polymerase II transcription cycle through CDK7 inhibition ameliorates inflammatory arthritis.

Macrophages are key drivers of inflammation and tissue damage in autoimmune diseases including rheumatoid arthritis. The rate-limiting step for transcription of more than 70% of inducible genes in macrophages is RNA polymerase II (Pol II) promoter-proximal pause release; however, the specific role of Pol II early elongation control in inflammation, and whether it can be modulated therapeutically, is unknown. Genetic ablation of a pause-stabilizing negative elongation factor (NELF) in macrophages did not affect baseline Pol II occupancy but enhanced the transcriptional response of paused anti-inflammatory genes to lipopolysaccharide followed by secondary attenuation of inflammatory signaling in vitro and in the K/BxN serum transfer mouse model of arthritis. To pharmacologically disrupt the Pol II transcription cycle, we used two covalent inhibitors of the transcription factor II H-associated cyclin-dependent kinase 7 (CDK7), THZ1 and YKL-5-124. Both reduced Pol II pausing in murine and human macrophages, broadly suppressed induction of pro- but not anti-inflammatory genes, and rapidly reversed preestablished inflammatory macrophage polarization. In mice, CDK7 inhibition ameliorated both acute and chronic progressive inflammatory arthritis. Lastly, CDK7 inhibition down-regulated a pathogenic gene expression signature in synovial explants from patients with rheumatoid arthritis. We propose that interfering with Pol II early elongation by targeting CDK7 represents a therapeutic opportunity for rheumatoid arthritis and other inflammatory diseases.

Performance of a hybrid capture-based target enrichment next-generation sequencing for the identification of respiratory pathogens and resistance-associated genes in patients with severe pneumonia.

Severe pneumonia remains the leading infectious cause of death worldwide. The time-consuming nature and suboptimal sensitivity of sputum cultures hamper prompt pathogen detection for tailored treatments. Advanced techniques such as polymerase chain reaction (PCR) and next-generation sequencing (NGS) offer rapid genetic pathogen detection and identification of antimicrobial resistance (AMR) genes. However, the performance of hybrid capture-based target enrichment NGS, e.g., Respiratory Pathogen ID/AMR Enrichment Panel (RPIP), for pathogen detection in patients with severe pneumonia remains uncertain. A prospective study involving adults with severe pneumonia was conducted. Respiratory samples from the lower respiratory tract were collected via bronchoalveolar lavage, bronchial washing, or endotracheal tube suction. The performance of RPIP in pathogen and AMR-associated gene detection was compared to that of conventional culture methods and the multiplex PCR-based FilmArray Pneumonia Panel (FilmArray-PN). A total of 83 subjects were enrolled. The most prevalent pathogens detected by RPIP were Rothia mucilaginosa, Stenotrophomonas maltophilia, Pseudomonas aeruginosa; herpes simplex virus-1, cytomegalovirus, and Epstein-Barr virus, and Pneumocystis jirovecii. Overall, the positive and negative agreement rates for bacterial detection were 63.6% and 97.5% between RPIP and culture methods, respectively, and 55.8% and 99.4% between FilmArray-PN and culture methods, respectively. Compared to FilmArray-PN, RPIP exhibited significantly better detection rates for bacteria (P = 0.029), viruses (P < 0.001), and fungi (P < 0.001) and identified additional blaOXA, blaCMY as extended-spectrum β-lactamase genes and blaOXA, blaSHV as carbapenemase genes. In conclusion, RPIP can sensitively profile respiratory pathogens and is a promising tool for detecting multiple microorganisms and AMR-associated genes in patients with severe pneumonia.IMPORTANCESensitive pathogen detection is pivotal for timely treatment by tailoring adequate antimicrobial agents. Unlike conventional phenotypic approach, novel measures using molecular interrogation appear promising. This study aimed to elucidate the efficacy of a hybrid capture-based target enrichment next-generation sequencing technique (Respiratory Pathogen ID/AMR Enrichment Panel, RPIP) as exemplified in a cohort with severe pneumonia. Pathogen landscape in the population was illustrated by these three methodologies. As compared with multiplex polymerase chain reaction-based FilmArray Pneumonia Panel and conventional culture, RPIP demonstrated significantly improved sensitivity in identifying bacteria, viruses, and fungi. The RPIP also exhibited better performance in identifying different pathogens in patients co-infected with multiple microorganisms. Additionally, the genotypes contributing to antimicrobial resistance were determined by RPIP. The study facilitated the implementation of molecular diagnosis by presenting real-world data, whereas future studies are mandated to generalize such an approach toward different clinical settings.

A cross-tissue transcriptome-wide association study reveals GRK4 as a novel susceptibility gene for COPD

Chronic obstructive pulmonary disease (COPD) is a prevalent respiratory disorder with environmental factors being the primary risk determinants. However, genetic factors also substantially contribute to the susceptibility and progression of COPD. Although genome-wide association studies (GWAS) have identified several loci associated with COPD susceptibility, the specific pathogenic genes underlying these loci, along with their biological functions and roles within regulatory networks, remain unclear. This lack of clarity constrains our ability to achieve a deeper understanding of the genetic basis of COPD. This study leveraged the FinnGen R11 genetic dataset, comprising 21,617 cases and 372,627 controls, along with GTEx V8 eQTLs data to conduct a cross-tissue transcriptome-wide association study (TWAS). Initially, we performed a cross-tissue TWAS analysis using the Unified Test for Molecular Signatures (UTMOST), followed by validation of the UTMOST findings in single tissues using the Functional Summary-based Imputation (FUSION) method and conditional and joint (COJO) analyses of the identified genes. Subsequently, candidate susceptibility genes were screened using Multi-marker Analysis of Genomic Annotation (MAGMA). The causal relationship between these candidate genes and COPD was further evaluated through summary data-based Mendelian randomization (SMR), colocalization analysis, and Mendelian randomization (MR). Additionally, the identified results were validated against the COPD dataset in the GWAS Catalog (GCST90399694). GeneMANIA was employed to further explore the functional significance of these susceptibility genes. In the cross-tissue TWAS analysis (UTMOST), we identified 17 susceptibility genes associated with COPD. Among these, a novel susceptibility gene, G protein-coupled receptor kinase 4 (GRK4), was validated through single-tissue TWAS (FUSION) and MAGMA analyses, with further confirmation via SMR, MR, and colocalization analyses. Moreover, GRK4 was validated in an independent dataset. This study identifies GRK4 as a potential novel susceptibility gene for COPD, which may influence disease risk by exacerbating inflammatory responses. The findings address gaps in previous single-tissue GWAS studies, revealing consistent expression and potential function of GRK4 across different tissues. However, considering the study’s limitations, further investigation and validation of GRK4’s role in COPD are warranted.

Plant Growth Promoting Microorganisms and Emerging Biotechnological Approaches for Sugarcane Disease Management

Sugarcane (Saccharum officinarum L.) is a highly valuable agricultural crop, cultivated globally in tropical and subtropical regions, primarily for its sugar content. Out of the 110 countries that grow sugarcane, India and Brazil together account for half of the world’s total production. Being an annual crop, it is prone to many diseases. The major diseases that can affect the sugarcane are red rot, wilt, sett rot, grassy shoot and pokkah boeng. Among the diseases Colletotrichum falcatum, Fusarium sacchari, Ceratocystis paradoxa, Candidatus Phytoplasma and Fusarium fujikuroi pathogen leads to more yield loss. Traditional disease management strategies, such as chemical treatments, conventional methods and biological control, offer limited protection throughout the crop cycle and raise concerns regarding environmental impact and sustainability. In recent years, plant growth-promoting microorganisms (PGPMs) have emerged as a promising alternative, offering environmentally friendly solutions to enhance plant health and manage diseases. RNAi has been explored to manage various diseases caused by viruses, fungi, and bacteria. By silencing key pathogenicity genes in the causal organisms, sugarcane mosaic virus (SCMV), smut, and leaf scald. The integration of PGPMs with RNAi emerging biotechnological tools and transcriptomics presents a sustainable approach to disease control, potentially reducing the dependency on chemical pesticides and promoting eco-friendly agricultural practices.

The Genomic Landscape of Wilson Disease in a Pan India Disease Cohort and Population-Scale Data.

Wilson's disease (WD) results from pathogenic ATP7B gene variations, causing copper accumulation mainly in the liver, brain, and kidneys. In India, despite studies on ATP7B variants, WD often goes undiagnosed, with the prevalence, carrier rate, and mutation spectrum remaining unknown. A multicenter study examined genetic variations in WD among individuals of Indian origin via whole exome sequencing. The study used the InDelible structural variants calling pipeline and conducted molecular dynamic simulations on variants of uncertain significance (VUS) in ATP7B AlphaFold protein structures. Additionally, a high-throughput gene screening panel for WD was developed. This study examined 128 clinically diagnosed cases of WD, revealing 74 genetically confirmed cases, 22 with ATP7B variants, and 32 without. Twenty-two novel ATP7B gene variants were identified, including a 322 bp deletion classified as a structural variant. Molecular dynamics simulations highlighted the potential deleterious effects of 11 ATP7B VUS. Gene burden analysis suggested associations with ANO8, LGR4, and CDC7. ATP7B gene hotspots for pathogenic variants were identified. Prevalence and carrier rates were determined as one in 18,678 and one in 67, respectively. A multiplex sequencing panel showed promise for accurate WD diagnosis. This study offers crucial insights into WD's genetic variations and prevalence in India, addressing its underdiagnosis. It highlights the novel genetic variants in the ATP7B gene, the involvement of other genes, a scalable, cost-effective multiplex sequencing panel for WD diagnosis and management and promising advancements in WD care.

Linalool and 1,8-Cineole as Constitutive Disease-Resistant Factors of Norway Spruce Against Necrotrophic Pathogen Heterobasidion Parviporum.

Norway spruce is an important coniferous species in boreal forests. Root and stem rot diseases caused by the necrotrophic pathogen Heterobasidion parviporum threaten the wood production of Norway spruce which necessitates the search for durable control and management strategies. Breeding for resistant traits is considered a viable long-term strategy. However, identification of potential resistant traits and markers remains a major challenge. In this study, short-term disease resistance screening was conducted using 218 Norway spruce clones from 17 families. Disease resistance was evaluated based on the size of necrosis lesion length following infection with the pathogen. A subset of needles/branches from clones with small (partial resistant) or large (susceptible) lesions were used for terpene analysis and transcriptomic profiling. The results revealed that the content of monoterpene linalool and 1,8-cineole and their respective encoded genes were significantly more abundant and highly expressed in the partial resistant group. Furthermore, linalool and 1,8-cineole were demonstrated to have inhibitory effect on the growth of the pathogen H. parviporum, with morphological distortion of the hyphae. RNAseq analysis revealed that transcript of pathogen genes involved in the regulation of carbohydrate metabolism and stress responses were significantly decreased in presence of the terpenes. The results suggest the relevance of monoterpenes together with jasmonic acid precursor and some genes involved in phenylpropanoid biosynthesis, as constitutive tolerance factors for Norway spruce tolerance against necrotrophic pathogen. The high level of necrosis related cell death gene expression might be factors critical for host susceptibility and disease development.

Abstract 4138455: Employing Bioinformatic Tools to Identify High-Risk Variants of Unknown Significance in Aortopathy Genes Associated with Aortic Dissection

Introduction: Pathogenic (P) or likely pathogenic (LP) aortopathy gene variants cause hereditary thoracic aortic aneurysm and dissection, but P/LP variants only explain approximately 20% of cases of thoracic aortic disease. Variants of unknown significance (VUS) are frequently identified among individuals undergoing genetic testing for thoracic aortic disease, however managing patients with VUSs remains clinically challenging. Hypothesis: Bioinformatic tools can be used to determine thresholds above which VUSs may be considered “high-risk.” Methods: Primary analyses were performed in the Penn Medicine Biobank (PMBB) which is composed of 43,731 participants who volunteered to have clinical information linked to biospecimen data including DNA which has undergone whole exome sequencing. PMBB participants were screened for VUSs in one of 11 aortopathy genes. VUS REVEL, AlphaMissense and minor allele frequency (MAF) high-risk thresholds were derived using cutpointR, a statistical package to optimize continuous variable thresholds based on binary outcomes. These thresholds were applied to VUS carriers in the PMBB and two independent validation cohorts. Logistic regression analysis was performed to test the association of high-risk VUSs with prevalent thoracic aortic disease. Results: There were 11,925 individuals in PMBB who carried at least one missense VUS. Carrying a VUS was associated with a modest increased risk of thoracic aortic aneurysm (TAA: OR=1.14, 95% confidence interval [CI] 1.01 to 1.29, P =0.034) but no increased risk of thoracic aortic dissection (OR=1.04, 95%CI 0.55 to 2.00, P =0.896). As VUS REVEL or AlphaMissense increased, or MAF decreased, the association between VUSs and thoracic aortic disease became statistically significant. Using cutpointR, we derived REVEL (&gt;0.649), AlphaMissense (&gt;0.2543), and MAF (&lt;8.16x10 -6 ) thresholds that together identified 435 high-risk VUSs robustly associated with prevalent dissection (OR=7.85, 95%CI 4.73 to 13.03, P &lt;0.001), though the association with TAA was attenuated (OR=2.35, 95%CI 1.62 to 3.42, P &lt;0.001). Similar results were observed in the UK Biobank (UKB) and Early Onset Sporadic Thoracic Aortic Dissection (ESTAD) cohorts. Conclusions: VUSs that met high-risk bioinformatic thresholds were strongly associated with prevalent aortic dissection in the PMBB, UKB and ESTAD. Future investigation is warranted to determine if these thresholds can instruct clinical care of individuals carrying aortopathy gene VUSs.

Clinical characteristics of urinary system symptoms in 11 patients with neuronal intranuclear inclusion disease

To summarize the characteristics of urinary system symptoms in 11 patients with neuronal intranuclear inclusion disease (NIID), in order to improve the understanding of the disease. A retrospective analysis was performed on 15 patients with NIID of the First Affiliated Hospital of Zhengzhou University, which were enrolled between January, 2020 and December, 2022. All of them were confirmed by NOTCH2NLC gene and pathology. GGC repeated expansion mutationof NOTCH2NLC gene, the pathogenic gene of NIID, was detected by gene test, and eosinophilic intranuclear inclusions were detected by skin pathological biopsy. 4/15 patients started with urinary symptoms, 11/15 patients with NIID combined with different degrees of urinary system symptoms, manifested as frequent urination, weak urination, incontinence and other neurogenic bladder symptoms, and the serious patients due to long-term urinary retention, secondary ureteral dilation, hydronephrosis, even renal failure, some patients with urinary system symptoms may be earlier than other systems.

BIOM-05. FUSION TRANSCRIPTOME LANDSCAPE IN GLIOBLASTOMA

Abstract BACKGROUND For most patients with glioblastoma (GBM), no truly effective salvage therapies exist. However, there are compelling examples in oncology where gene fusions lead to functioning oncoproteins that are highly effective targets (ie BCR-ABL1 in CML). Using a large genomic database, we sought to determine the prevalence of fusion transcripts in GBMs. METHODS A total of 4392 GBMs were tested at Caris Life Sciences (Phoenix, AZ). Mutations were detected by NextGen sequencing of DNA (592-gene panel or whole exome sequencing); gene fusions were detected by Whole Transcriptome Sequencing. All tumors were wild type for IDH1/2. Significance was tested by Fisher-Exact and ChiSquare and adjusted by Benjamini-Hochberg (q &amp;lt;0.05). RESULTS Overall, pathogenic fusions were found in 428 (9.7%). The most prevalent were FGFR3 [N=159 (37%), highest FGFR3:TACC3, N=134], MET [N=92 (21%), highest PTPRZ1:Met, N=31; ST7:MET N=25; CAPZA2: MET, N=23), EGFR [N=87(20%), highest EGFR:SETP14, N=21 and SEC61G: EGFR, N=19], NTRK2 (N=27), PDGFRA (N=23), ROS1 (N=14) and BRAF (N=10). Other actionable fusions including ALK (N=3), NTRK3 (N=3), RAF1(N=3), RET (N=3), NTRK1(N=2) were seen. Tumors with fusions were more likely to have pathogenic gene amplifications including: MET (7.5% vs. 0.7%), FGFR3 (5% vs. 0.2%), CDK4 (17% vs. 11%) and MDM2 (12% and 7.5%) but less frequent EGFR mutation (6.1% vs. 18%), amplification (6.1% vs. 18%) and EGFRvIII mutation (11.9% vs. 22.5%), RB1 (2.9% vs. 11.5%) and TP53mutation (22% vs. 30%) (all q&amp;lt;0.05). EGFR fusions are enriched with EGFR amplification (92%) and EGFRvIII mutation (51%); cMET fusion with MET amplification (40%). CONCLUSIONS Comprehensive molecular profiling reveals that approximately 10% of IDH WT GBMs carry oncogenic fusions that may be therapeutic targets. Broad spectrum of observed fusions underscores the need for novel clinical trial designs to allow efficient enrollment for prospective testing of potential targeted agents.

Research progress on inherited distal renal tubular acidosis due to variants of V-ATPase-related genes

V-ATPases are a class of multi-subunit protein complexes that utilize energy derived from ATP hydrolysis for mediating H+ transport across cell membranes, which plays an important role in a range of life activities by acidifying the intracellular and extracellular environment. Variants of V-ATPase genes may lead to complete or partial loss of V-ATPase activity, which in turn may impair the ability of type A intercalated cells in renal tubules to pump H+ into the tubular lumen, ultimately resulting in the onset of autosomal recessive distal renal tubular acidosis (dRTA). With the rapid development of molecular techniques, ATP6V0A4 and ATP6V1B1 have now been identified as the pathogenic genes for dRTA. Moreover, animal and cell experiments have substantiated the implication of V-ATPase subunit genes including ATP6V1C2 and ATP6V1G3 in the development of dRTA, though clinical evidence is still limited. This article has reviewed recent progress on the genetic and molecular mechanisms of V-ATPase subunit gene variants which can lead to dRTA, which may shed light on the diagnosis and treatment of this disease.

Clinical phenotype and genetic analysis of a child with partial duplication of 10q and a literature review

To explore the clinical phenotype and pathogenesis of a child with partial duplication in the long arm of chromosome 10 (10q), and conduct a review of relevant literature. A child presented at Lianyungang Maternal and Child Health Care Hospital in April 2018 for growth retardation, intellectual disability, and autism spectrum disorder (ASD) was selected as the study subject. Peripheral blood samples were collected from the child and his parents for G-banded chromosomal karyotyping analysis. Genomic DNA was also extracted for chromosomal microarray analysis (CMA). The clinical phenotype and relevant genes were searched in the Online Mendelian Inheritance in Man (OMIM) and the UK Database of Genomic Variation and Phenotype in Humans using Ensembl Resources (DECIPHER). The pathogenicity of chromosomal variation was analyzed based on guidelines from the American College of Medical Genetics and Genomics (ACMG). Relevant literature was searched from the CNKI, Wanfang Data, and PubMed databases by using keywords such as "10q" "duplication" and "trisomy", with the time set as from the establishment of database to December 1, 2023. This study has been approved by the Medical Ethics Committee of the Lianyungang Maternal and Child Health Care Hospital (No. XM2023030). The clinical phenotype of child had included growth retardation, intellectual disability, and ASD. G-banded chromosomal analysis suggested that the child has a karyotype of 46,XY,dup(10)(q23.31q24.33), whilst both of his parents were normal. CMA analysis of the child revealed that the child was arr[19]10q23.31q24.33(87603382_104948862)×3, with a 17.34 Mb duplication in the 10q23.31q24.33 region. Search of the OMIM database suggested that the duplicated segment has contained 171 genes associated with various diseases, and search of the DECIPHER database has identified cases with overlapping with the duplication. A search of the PubMed database has identified 2 publications involving 2 patients with chromosomal duplications overlapping the 10q23.31q24.33 region with a segment length of > 10 Mb. The 2 patients had mainly manifested growth retardation, intellectual disability, ASD, and facial and limb malformations. The main pathogenic genes had included PTEN, WNT8B, LZTS2, NFKB2, PAX2, KIF11, FRA10AC1, and CNNM2. No similar case was retrieved from the CNKI and Wanfang Data databases. The partial 10q duplication as a novel CNV involving genes such as PTEN and WNT8B probably underlay the growth retardation, intellectual disability and ASD in child 1 . This study has enriched the genotype-phenotype spectrum of patients with partial 10q23.31q24.33 duplications.

Development of a novel strategy to reduce diagnostic errors in real-time polymerase chain reaction using probe-based techniques

Real-time PCR assays are valuable tools for the rapid and accurate diagnosis of infectious diseases by identifying the nucleic acid sequences of pathogens. Here, we aimed to develop a recombinant plasmid-based standard for validating the sensitivity of different molecular diagnostic methods adopting the Jonstrup assay (J assay). Chimeric plasmid DNA (cpDNA) harboring various pathogen genes and the target site of the J assay was constructed. Our findings revealed that the J assay could detect a single copy of the target gene similar to digital droplet PCR. The detection sensitivity of each established real-time PCR method for various disease diagnoses was evaluated using the cpDNA. Although most methods showed high sensitivity, similar to that of the J assay, the VHS Garver and SARS-CoV-2 diagnostic methods exhibited detection sensitivities tenfold lower than that of the J assay. To ensure accuracy of results and avoid genetic contamination from positive controls, we introduced an additional probe attachment site emitting distinct fluorescent signals within the cpDNA. Target genes and exogenous sequences within the plasmid DNA were simultaneously detected in a single assay using this unique method. Our approach will help improve the sensitivity of diagnostic methods and develop novel diagnostic methods based on molecular techniques.

Analysis of TRIOBP gene in non-syndromic deafness: A case report.

Through family investigation, the genetic map was drawn and audiological characteristics were analyzed. High-throughput sequencing was used to screen the deafness genes of the proband. Sanger sequencing was used to verify the suspected pathogenic sites in the family. Identify the causes of hearing loss and treatment options. Bilateral moderate to severe sensorineural deafness. After completing the examination, the patient was recommended to wear a hearing aid or do a cochlear implant, but the patient was not treated for personal reasons. All 8 patients in this family were nonsyndromic deafness. The proband had a compound heterozygous mutation of c.A4484T/c.A4510G in the TRIOBP gene, and the patient II-6 had a heterozygous mutation of c.A4484T in the TRIOBP gene. A complex heterozygous mutation of TRIOBP gene c.A4510G/c.G59T was found in II-7, but no reports of pathogenicity of these mutations were found in relevant literatures and databases. In addition, patients II-6, III-4, and III-6 had heterozygous mutations of CHD7 gene c.T2615C and C.3202-5T >C, and patients II-6 and III-4 also had heterozygous mutations of CHD23 gene c.G5312A and c.C6250T. In this study, a new locus of the TRIOBP gene was found, which enriched the gene mutant spectrum and clarified the pathogenic gene of the proband. However, the etiology of deafness in other members of the family needs to be further analyzed.

Genomic insights into bamboo witches' broom disease: pathogenicity and phytohormone biosynthesis in Aciculosporium take.

Bamboo witches' broom disease (WBD), caused by Aciculosporium take Miyake, devastates bamboo forests. Understanding the genome and pathogenic factors of pathogen is crucial for disease control. We employed single-molecule real-time sequencing, Illumina paired-end sequencing, and chromatin interaction mapping techniques to assemble the genome of A. take CCTCC-M2023413, analyze pathogenicity- and phytohormone-biosynthesis-related genes, and compare it to 12 other WBD pathogens. The genome of A. take is 59.24 Mb in size, with 54.32% repeats, 7 chromosomes, 7,105 protein-coding genes, 84 ribosomal RNAs, and 115 transfer RNAs. Predictive analysis of pathogenicity genes found 237 carbohydrate-active enzymes, 1,069 membrane transport proteins, 1,040 pathogen-host interaction genes, 315 virulence factors, and 70 effectors. Most of pathogenicity genes overlapped with repeat-rich regions. Additionally, 172 genes were linked to auxin biosynthesis, 53 to brassinosteroid biosynthesis, and 2 to cis-zeatin biosynthesis. Comparative genomic analysis identified 77 core orthogroups shared by 13 WBD pathogens, played roles in metabolites, genetic information processing, pathogenesis, cis-zeatin biosynthesis, lifespan, and quorum sensing. The miaA gene, crucial for cis-zeatin biosynthesis, is structurally conserved and sequence-diverse among 13 WBD pathogens, with upregulated expression during bamboo WBD pathogenesis. This highlights that cis-zeatin is significant contributor to host pathogenesis, and miaA is a new potential target for controlling WBD. This study provides important insights on preventing and controlling bamboo WBD.

Prevalence of transthyretin cardiac amyloidosis in undifferentiated heart failure with preserved ejection fraction.

Transthyretin amyloid cardiomyopathy (ATTR-CM) is an increasinglyrecognized cause of heart failure with preserved ejection fraction (HFpEF), which may be diagnosed non-invasively using 99 mTc 3,3-diphosphono-1,2-propanodicarboxylic acid (DPD) scintigraphy-based diagnostic criteria. Our aim was to determine the prevalence of ATTR-CM in an undifferentiated HFpEF cohort with a DPD scintigraphy-based screening protocol. Patients with HFpEF [ejection fraction (EF) ≥50%] aged ≥60years and no prior evaluation for cardiac amyloidosis or known monoclonal gammopathy attending a regional cardiology network were screened with DPD scintigraphy. Patients with positive myocardial uptake (Perugini grade 2 or 3) were tested for a monoclonal protein and transthyretin gene variant. Eighty-six subjects were prospectively enrolled: 56% female, mean age 77±8years, 63% New York Heart Association (NYHA) Class III and median N-terminal pro-brain natriuretic peptide (NT-proBNP) 1766ng/L [inter-quartile range (IQR) 731-3703]. DPD scintigraphy was positive in seven patients (8%). Monoclonal gammopathy of undetermined significance was present in one out of seven patients, and no pathogenic TTR gene variant was identified. The prevalence of wild-type ATTR-CM was 8% of this cohort. Compared with the HFpEF DPD scintigraphy-negative cohort, DPD scintigraphy-positive patients were older (86±3 vs. 76±8years), more frequently male (16% vs. 2%, P=0.02), and had significantly greater left ventricular (LV) wall thickness (16 vs. 12mm; P=0.002) and higher high-sensitivity troponin levels at diagnosis [78ng/L (IQR 21-116) vs. 11ng/L (IQR 9-17); P<0.001]. In an undifferentiated HFpEF cohort, 8% were found to have wild-type ATTR-CM using a DPD scintigraphy-based screening protocol. Screening undifferentiated HFpEF patients is associated with a significant diagnostic yield, which can be further increased by targeting older males with increased LV wall thickness and elevated high-sensitivity troponin levels.