Search PubMed⌕ Search

SEARCH · Search PubMed

Results for “Pathogenic variant”

Search indexed PubMed citations on genomics, clinical trials, systematic reviews and public health. Explore titles, authors and supplied subject terms, then open the PubMed record.

Quote a phrase for an exact phrase match. Source license links do not imply unrestricted reuse.

At least 649 records · Page 36Linked to original sources
PubMed2003

Direct interferon-gamma-mediated protection caused by a recombinant coxsackievirus B3.

Coxsackievirus B3 (CVB3) is one of the most important causes of viral myocarditis. Cytokines are involved in the control of CVB3 replication and pathogenesis. Local expression of specific cytokines by recombinant CVB3 confers prevention of virus-caused myocarditis. Expression of IFN-gamma by CVB3(IFN-gamma) protected BALB/c and C57BL/6 mice when the lethal infection with the highly pathogenic CVB3H3 variant was given directly after or prior to CVB3(IFN-gamma) inoculation by decreasing the viral load and spread as well as tissue destruction. This direct effect was not restricted to the homologous virus. In vitro, cocultivation of CVB3(IFN-gamma)-infected cells induced a reduction of CVB3H3 replication and virus-induced cytopathogenicity.

Animals↗
PubMed2001

An improved method for detection and quantification of differential interactions between poliovirus internal ribosome entry site RNA and pyrimidine tract binding protein from primary cells.

Attenuated and pathogenic viral variants are often extremely similar viruses with drastically different replication potentials. Despite precise knowledge of viral residues responsible for poliovirus attenuation/neurovirulence, molecular mechanisms mediating these effects remain poorly understood. Data from numerous sources suggest that a functional difference in translation initiation is one responsible factor. However, direct evidence, as well as a comprehensive model are lacking. Several difficulties, including lack of an assay system to quantify differential internal ribosome entry site/pyrimidine tract binding protein interaction in relevant systems, have precluded progress. A novel assay system that overcomes some difficulties is presented below. The assay uses streptavidin paramagnetic particles, biotinylated RNA and glutathione-S-transferase/pyrimidine tract binding protein fusion to detect nanogram levels of uncloned cellular pyrimidine tract binding protein species that interact with internal ribosome entry site RNA. Using this assay, it was shown that pyrimidine tract binding protein from primary human monocytes binds to internal ribosome entry site RNA from virulent poliovirus better than to that from attenuated virus, while pyrimidine tract binding protein from HeLa cells does not distinguish between the two internal ribosome entry sites. Since primary human monocytes reflect neurovirulence-related differential poliovirus replication, these results suggest that pyrimidine tract binding protein may contribute to differential poliovirus replication in vivo. This assay also has the potential to be applicable broadly to other nucleic acid/protein interactions.

5' Untranslated Regions↗
PubMed2001

Germline and somatic mutations in hMSH6 and hMSH3 in gastrointestinal cancers of the microsatellite mutator phenotype.

Hereditary and sporadic gastrointestinal cancer of the microsatellite mutator phenotype (MMP) is characterized by a remarkable genomic instability at simple repeated sequences. The genomic instability is often caused by germline and somatic mutations in DNA mismatch repair (MMR) genes hMSH2 and hMLH1. The MMP can be also caused by epigenetic inactivation of hMLH1. The MMP generates many somatic frameshift mutations in genes containing mononucleotide repeats. We previously reported that in MMP tumors the hMSH6 and hMSH3 MMR genes often carry frameshift mutations in their (C)(8) and (A)(8) tracks, respectively. We proposed that these 'secondary mutator mutations' contribute to a gradual manifestation of the MMP. Here we report the detection of other frameshift, nonsense, and missense mutations in these genes in colon and gastric cancers of the MMP. A germline frameshift mutation was found in hMSH6 in a colon tumor harboring another somatic frameshift mutation. Several germline sequence variants and somatic missense mutations at conserved residues were detected in hMSH6 and only one was detected in hMSH3. Of the three hMSH6 germline variants in conserved residues, one coexisted with a somatic mutation at the (C)(8) track and another had a somatic missense mutation. We suggest that some of these germline and somatic missense variants are pathogenic. While biallelic hMSH6 and hMSH3 frameshift mutations were found in some tumors, many tumors seemed to contain only monoallelic mutations. In some tumors, these somatic monoallelic frameshift mutations at the (C)(8) and (A)(8) tracks were found to coexist with other somatic mutations in the other allele, supporting their functionality during tumorigenesis. However, the low incidence of these additional somatic mutations in hMSH6 and hMSH3 leaves many tumors with only monoallelic mutations. The impact of the frameshift mutations in gene expression was studied by comparative analysis of RNA and protein expression in different tumor cell clones with different genotypes. The results show that the hMSH6 (C)(8) frameshift mutation abolishes protein expression, ruling out a dominant negative effect by a truncated protein. We suggest the functionality of these secondary monoallelic mutator mutations in the context of an accumulative haploinsufficiency model.

Amino Acid Sequence↗
PubMed1996

Permissiveness of human embryonal fibroblasts for coxsackieviruses B3. Investigations on virus genetic markers in vitro and localization of virus receptor distribution by immunogold replica technique.

In our previous paper (29) we could show, that the replication of four Coxsackie B3 virus strains in human fibroblast lines from different origin was dependent on both the virus strain and the cell line used. Although generally no cytopathic effect could be observed out of one virus strain more pathogenic virus variants could be selected able to destroy virus-sensitive as well as insensitive fibroblasts. The present study was designed to characterize these virus strains by using several in vitro genetic markers. Differences were found concerning plaque size and the temperature marker, whereas the other markers (d, DD, DEAE-D) remained constant. Furthermore, these models of persistent as well as lytic CVB3 infection were analysed by immunoelectron microscopy to study the interaction of viral ligands with cellular receptors. The qualitative and quantitative differences in adsorption of the CVB3 strains to two human fibroblast lines as well as to HeLa cells corresponded well with the virological results. They underline that even in vitro in human cell lines of different origin changes in distribution, quantity and quality of receptors were demonstrable forming the base for the various virus sensitivity.

Animals↗
PubMed2001

Superoxide dismutase gene mutations in Italian patients with familial and sporadic amyotrophic lateral sclerosis: identification of three novel missense mutations.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder affecting motor neurons. The majority of the patients are sporadic cases (SALS), while 5-10% of the patients have a family history of ALS (familial ALS or FALS). Mutations in the gene coding for cytoplasmic Cu/Zn superoxide dismutase (SOD1) have been identified in about 20% of FALS cases. We found SOD1-gene mutations in five of 34 unrelated FALS, and in two of 44 SALS patients. Three FALS patients carried the previously described A4V (two cases) and L84F mutations (one case), while two FALS patients carried new missense mutations: a G12R substitution in exon 1, and a F45C substitution in exon 2, respectively. The newly identified mutations were both associated with a slowly progressive disease course. Two SALS patients carried the homozygous D90A and the heterozygous I113T mutation, respectively. In addition, in one SALS patient we identified an A95T amino acid substitution, that is apparently a non-pathogenic SOD1 variant. Our study increases the number of ALS-associated SOD1 gene mutations.

Adult↗
PubMed2026

Retinopathy caused by a primary immune regulatory disorder - the spectrum of AIRE-associated retinopathy: case series and literature review.

BACKGROUND/OBJECTIVE: Retinal involvement in autoimmune polyendocrine syndrome type 1 (APS1), a rare monogenic autoimmune disorder caused by mutations in the AIRE gene, is increasingly recognised but remains poorly defined. Prior reports suggest a variable phenotype, ranging from mild changes to severe vision loss, often presumed untreatable. We explored the range of retinal phenotypes associated with AIRE gene deficiency in a multicentre case series of patients with APS1. METHODS: We performed a retrospective case note review of patients with molecularly confirmed APS1 from tertiary ophthalmic centres. Clinical history, multimodal retinal imaging, electrophysiology, genetic data, and treatment regimens were analysed. Histopathology was available in one case postmortem. RESULTS: Records were reviewed from five unrelated female patients. Median age was 14 years at onset of ocular involvement and 33 years at most recent follow up. Some findings from two cases have been previously reported. Three distinct pathogenic AIRE variants contributing to biallelic genotypes were observed. Retinal findings ranged from structurally and functionally normal to advanced degeneration. One patient demonstrated sharp zonal atrophy on histopathology. Inflammatory features predominated in two cases, both showing durable vision preservation with periocular or systemic immunomodulation. One patient demonstrated four years of disease stabilisation with rituximab. No consistent genotype-phenotype correlation emerged. CONCLUSION: AIRE-associated retinopathy encompasses a diverse spectrum, from clinically silent to profound degeneration. Early, targeted immunomodulation might preserve vision in selected cases. These findings advocate for ophthalmic surveillance in APS1, and support further investigation into predictive biomarkers and possible tailored immunotherapy in this vision-threatening autoimmune disorder.

Humans↗
PubMed2025

A streamlined base editor engineering strategy to reduce bystander editing.

Base editing (BE) can permanently correct over half of known human pathogenic genetic variants without requiring a repair template, thus serving as a promising therapeutic tool to treat a broad spectrum of genetic diseases. However, the broad activity windows of current base editors pose a major challenge to their therapeutic application. Here, we show that integrating a naturally occurring oligonucleotide binding module into the deaminase active center of TadA-8e, a highly active deoxyadenosine deaminase, enhances its editing specificity. When conjugated with a Cas9 nickase or alternative PAM Cas9 variants, the engineered TadA variant-TadA-NW1-consistently achieves robust A-to-G editing efficiencies within an editing window consisting of four nucleotides, substantially narrower than the 10-bp editing window of the TadA-8e-derived ABEs. Moreover, compared to ABE8e, ABE-NW1 shows significantly decreased Cas9-dependent and -independent off-target activity while maintaining similar on-target editing efficiency. Further, TadA-NW1 can be reprogrammed to perform desired cytidine deamination and adenine transversion within a restricted editing window. Finally, in a cystic fibrosis (CF) cell model, ABE-NW1 outperforms existing ABEs in accurately and efficiently correcting the CFTR W1282X variant, one of the most common CF-causing mutations. In all, we engineered a suite of base editors with refined activity windows, enabling more precise base editing. Importantly, this study presents a streamlined genome editor re-engineering strategy to accelerate the development of therapeutic base editing.

Gene Editing↗
PubMed2026

Analysis of 14q12 microdeletions reveals novel regulatory loci for the neurodevelopmental disorder-related gene FOXG1.

Up to 17% of neurodevelopmental disorders (NDDs) can be explained by pathogenic structural variants (SVs) that disrupt coding regions and elicit gene dosage defects. However, noncoding SVs which can perturb cis-regulatory elements (CREs) and downstream gene expression are understudied. In this study, we describe multiple 14q12 deletions downstream of NDD-related gene FOXG1 in individuals with overlapping phenotypes of FOXG1 haploinsufficiency. We show that deletion of a minimum region of overlap (MRO) reduced FOXG1 expression, disrupted CREs and altered FOXG1's native genomic interactions. Deleting the MRO did not fully eliminate FOXG1 expression, indicating that multiple CREs likely cooperate to regulate FOXG1 and would need to be deleted to completely prevent expression. The transcriptomic profiles of MRO loss overlap in part with FOXG1 loss, including direct FOXG1 targets, indicating converging molecular pathways. These findings expand the scope of FOXG1's complex regulatory region, and more broadly, of regulatory SVs in NDD susceptibility.

Forkhead Transcription Factors↗
PubMed2026

Sequential gene loss promotes expansion of monophasic Salmonella Typhimurium ST34.

Understanding the genetic factors facilitating emergence of infectious diseases is critical, however, mechanisms underlying expansion of pathogenic bacterial variants remain unclear. Here we performed a large-scale genomic analysis of 44,597 Salmonella Typhimurium genomes and observe that sequential gene loss in monophasic Salmonella Typhimurium (mSTM) ST34 explains its clonal expansion as an increasingly prevalent zoonotic lineage. Functional and in vivo competition experiments show that a frameshift mutation in dinB, a polymerase for translesion DNA synthesis, leads to transcriptional changes affecting flagellin gene expression and subsequent loss of the flagellin-encoding fljB, altering the requirements for gut infection. Temporal evolutionary modelling supports a role for gene loss events in a specific chronological order for mSTM ST34 expansion. Our findings reveal a stepwise pathoadaptation model underpinning clonal global spread, providing mechanistic insights relevant to forecasting future pandemics.

Journal Article↗
PubMed2001

Results of an open, non-placebo controlled pilot study investigating the immunomodulatory potential of autovaccine.

Autovaccines are prepared from autologous, human, non-pathogenic, "rough" variants of E. coli derived from the stool flora of individuals according to a highly standardized procedure. As a fundamental concept within microbiological therapy, these autovaccines are mainly used to treat chronic inflammatory disorders associated with impaired immune reactions resistant to standard therapeutic treatments. Generally, immunomodulatory effects of outer membrane components or cell wall fragments of gram-negative bacteria on innate or adaptive immunity are widely accepted but nevertheless mechanisms of actions of these autovaccines remained obscure, despite some recent publication about other autovaccine preparations of different origin. Hence, immunomodulating properties of autovaccine were investigated in a pilot study with 78 outpatients with variable disorders ranging from recurrent respiratory infections to diffuse gastrointestinal complaints. Patients received their autologous bacteria parenterally in increasing doses. Before application and 4 to 6 weeks after application of autovaccine, blood samples of the patients were taken to investigate a range of immunological parameters such as acute phase proteins, serum antibodies and cytokines. The results revealed that autovaccines were able to modulate significantly the release of three potent immunoregulatory cytokines e.g. interferon-gamma, granulocyte-macrophage-colony stimulating factor and interleukin-1 beta, whereas specific humoral immunity remained largely unaffected. From these results it may be concluded that the autovaccine mainly act antigen non-specifically on the cytokine level rather than inducing a specific vaccination. Further studies with more detailed kinetic measurements of cytokines will have to verify these results.

Acute-Phase Reaction↗
PubMed1989

An altered v-raf is required in addition to v-myc in J3V1 virus for acceleration of murine plasmacytomagenesis.

We have isolated and molecularly cloned a highly pathogenic virus variant, J3V1, from murine plasmacytomas induced by a combination of pristane and the weakly transforming recombinant retrovirus J3. J3 virus is a derivative of the v-raf/v-myc-carrying J2 virus that was generated by a frameshifting deletion inactivating v-raf in J2. J3V1 contains an additional deletion of 334 base paris in gag, which restores the correct reading frame for v-raf and results in the expression of a p57 gag-raf fusion protein. Reactivation of v-raf in J3 is required for efficient plasmacytoma acceleration in pristane-conditioned BALB/cAn mice.

Amino Acid Sequence↗
PubMed2006

Conversion efficiency of bank vole prion protein in vitro is determined by residues 155 and 170, but does not correlate with the high susceptibility of bank voles to sheep scrapie in vivo.

The misfolded infectious isoform of the prion protein (PrP(Sc)) is thought to replicate in an autocatalytic manner by converting the cellular form (PrP(C)) into its pathogenic folding variant. The similarity in the amino acid sequence of PrP(C) and PrP(Sc) influences the conversion efficiency and is considered as the major determinant for the species barrier. We performed in vitro conversion reactions on wild-type and mutated PrP(C) to determine the role of the primary sequence for the high susceptibility of bank voles to scrapie. Different conversion efficiencies obtained with bank vole and mouse PrP(C) in reactions with several prion strains were due to differences at amino acid residues 155 and 170. However, the conversion efficiencies obtained with mouse and vole PrP(C) in reactions with sheep scrapie did not correlate with the susceptibility of the respective species to this prion strain. This discrepancy between in vitro and in vivo data may indicate that at least in the case of scrapie transmission to bank voles additional host factors can strongly modulate the species barrier. Furthermore, in vitro conversion reactions with different prion strains revealed that the degree of alteration of the conversion efficiency induced by amino acid exchanges was varying according to the prion strain. These results support the assumption that the repertoire of conformations adopted by a certain PrP(C) primary sequence is decisive for its convertibility to the strain-specific PrP(Sc) conformation.

Amino Acid Sequence↗
PubMed2004

A cross-sectional serological survey of the Dutch commercial poultry population for the presence of low pathogenic avian influenza virus infections.

After the discovery of poultry infected with highly pathogenic avian influenza (HPAI) virus of subtype H7N7 in the central area of The Netherlands on 28 February 2003, the hypothesis was put forward that an outbreak of the low pathogenic (LP) variant of H7N7 had preceded, unnoticed, the occurrence of the HPAI virus. Consequently, a cross-sectional serological survey of the Dutch poultry population was executed in the second week of March 2003. The basic requirements set were detection of a 5% prevalence of flocks exposed to LPAI virus with 95% confidence within the production type stratification level within each province in The Netherlands. Because of supposed higher risk of avian influenza infections in ducks, turkeys and free-range poultry, all the commercial flocks of these production types present in The Netherlands were sampled. The serological screening of 28018 sera from 1193 randomly selected poultry farms, located outside surveillance zones showed that LPAI H7 virus infections had occurred on three neighbouring farms all located in the southwest of The Netherlands. No antibodies against the neuraminidase N7 subtype were detected in the sera of these farms, indicating that the subtype was different from the HPAI H7N7 subtype that caused the avian influenza epidemic in 2003. In addition, evidence of infections with non-H5 or non-H7 subtypes of influenza A virus were obtained in two other farms located in the northeast and the southeast of The Netherlands. It was concluded that the HPAI subtype H7N7 outbreak was most likely not preceded by a significant circulation of a LPAI subtype H7N7 virus. Based on the Dutch experience, recommendations are made to detect avian influenza infections faster in the future.

Animals↗
PubMed2001

Genetics of ALS in Italian families.

Amyotrophic lateral sclerosis (ALS) is a progressive neurodegenerative disorder affecting motor neurons. The majority of the patients are sporadic cases (SALS), while 10-15% of patients has a family history of ALS (familial ALS or FALS). Mutations in the gene coding for cytoplasmic Cu/Zn superoxide dismutase (SOD1) have been identified in 20% of FALS. We found SOD1-gene mutations in 7 of 36 unrelated FALS and in 3 of 48 SALS patients. Four FALS patients carried previously described mutations, the A4V (2 cases), the L84F mutations (1 case), and the G93D (1 case), while three FALS patients carried new missense mutations: the G12R mutation, the F45C mutation and the V47F mutation, respectively. Two SALS patients carried previously reported mutations: the homozygous D90A and the heterozygous I113T mutation, respectively. In addition, in one SALS patient we identified an apparently non-pathogenic SOD1 variant: the A95T mutation. Our study contributes to expand the number of ALS-associated SOD1 gene mutations.

Adult↗
PubMed2026

Protein sorting and proteostasis mechanisms in CFTR-related exocrine pancreas dysfunction: A systematic narrative review.

The pancreas consists of exocrine and endocrine compartments. In the exocrine pancreas, cystic fibrosis transmembrane conductance regulator (CFTR) functions mainly in ductal epithelial cells as a chloride and bicarbonate channel. Its activity depends on proper protein folding, trafficking, and localization to the apical membrane. This systematic narrative review aims to synthesize the available evidence on the role of protein sorting machinery in CFTR channelopathies and its contribution to exocrine pancreatic dysfunction. A thorough search was conducted using PRISMA criteria on PubMed, Wiley Online Library, and Scopus for studies published in English between January 2000 and November 2025. Twenty studies that met the inclusion criteria were included in this review. Pathogenic CFTR variants impair protein folding, endoplasmic reticulum (ER) exit, and endosomal recycling, resulting in reduced apical membrane expression and stability. These defects disrupt the localization of associated transporters and secretory proteins, impair ductal bicarbonate secretion, alter zymogen handling, and promote acinar injury, although these claims are supported mainly by indirect experimental models and therefore require clinical confirmation. CFTR channelopathies in the exocrine pancreas encompass both ion transport defects and broader disruptions of protein sorting machinery. CFTR may contribute to the assembly, stabilization, or localization of selected apical transport complexes, and its loss can secondarily alter epithelial organization. Therapeutic approaches targeting both channel correction and intracellular trafficking may improve pancreatic function and mitigate disease progression.

Humans↗
PubMed2026

Enhanced risk stratification in hypertrophic cardiomyopathy through the integration of extracellular volume fraction on cardiovascular magnetic resonance.

AIMS: This study investigated the incremental prognostic value of cardiovascular magnetic resonance (CMR)-derived extracellular volume fraction (ECV), a marker of diffuse interstitial fibrosis, beyond late gadolinium enhancement (LGE) in hypertrophic cardiomyopathy (HCM). METHODS AND RESULTS: We analysed 990 consecutive HCM patients (median age 58 years, male 68.3%) who underwent CMR between 2012 and 2024. LGE and global ECV were quantified, and their associations with the primary endpoint of HCM-related events-a composite of sudden cardiac death (SCD) events, heart failure (HF) events, and HCM-related death-were assessed. During a median follow-up of 3.2 years, 64 (6.5%) patients experienced the primary endpoint. While LGE (median 7.1%, IQR 2.3-16.9%) and ECV (median 29.0%, IQR 26.6-32.0%) were moderately correlated (R = 0.604, P < 0.001), both were significantly associated with increased risk of the primary endpoint and individual outcomes of SCD and HF events, and optimal cutoffs were determined as LGE &#x2265; 27% and ECV &#x2265; 35%. Patients with ECV &#x2265; 35% had more symptoms, a more severe phenotype with greater systolic and diastolic dysfunction, and more pathogenic gene variants. Notably, ECV remained a significant predictor of the primary endpoint (adjusted HR 1.08, 95% CI 1.02-1.15, per 1%) after adjustment for key disease variables, including left ventricular ejection fraction and LGE. Elevated ECV effectively identified high-risk individuals even among lower-risk subgroups, including those with low LGE burden. CONCLUSION: Increased ECV is an independent predictor of HCM-related outcomes. ECV may serve as a novel imaging biomarker to refine risk stratification in HCM patients who do not meet traditional LGE-based high-risk criteria.

Humans↗