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Petrovski, S.

Publications and source records attributed to Petrovski, S..

At least 19 recordsLinked to original sources

Identification of novel enolase negative Segatella copri subspecies supports notion of Segatella copri speciation via alternative phosphoenolpyruvate synthesis pathways

BackgroundSegatella copri is characterised as a prominent glycolytic plant-based fiber utiliser within the human gut. My recent work has introduced a new interpretation of the positive impacts of plant-based polysaccharides on S. copri, as a significant negative relationship between S. copri and Blautia spp. was identified. The high rate of electron donor consumption by Blautia spp. indicated that competition for the electron donors, formate, ferredoxin and fumarate, could be the route of the negative relationship but would also explain the positive relationship with plant-based polysaccharides, as they are products of fiber fermentation intestinally. MethodsForty two genomes of S. copri were annotated via Prokka to identify alternative PEP pathways. Phylogenetics allowed effectively classification of the S. copri isolates into species and subspecies clusters. The sequence homology of nucleotides and proteins were analysed against the control, S. copri DSM 18205, to determine the level of conservation in the alternative phosphoenolpyruvate synthesis pathways. ResultsEnolase (eno) was not identified in the S. copri strains; JCM 13468, LKV-178-WT-2C, RHA03, RHA01 and RHA02, and the whole genome phylogenetic grouping of these strains, has proposed the existence of an eno(-) subspecies of S. copri. This work furthered this idea by identifying alternative PEP pathways from formate, ferredoxin and fumarate, which were the most conserved in the eno(-) S. copri genomes. ConclusionThis work has provided rationale to why enolase may not be present within the eno(-) S. copri isolates and have shown that these alternative PEP synthesis pathways could negate the requirement of enolase in cells and may be factor in evolution of S. copri metabolism.

evolutionary biology↗

A Novel Pilus System in Candidate Phyla Radiation Bacteria

The Candidate Phyla Radiation (CPR) represents a bacterial superphylum estimated to include between 15-50% of all bacterial species, yet CPR bacteria remain challenging to culture and have been primarily identified through metagenomic approaches. Candidatus Mycosynbacter amalyticus is a parasitic CPR bacterium that specifically targets Gordonia amarae, an actinobacterium with a hydrophobic, mycolic acid-rich cell envelope. Previous cryo-electron tomography indicated that Ca. M. amalyticus assembles thin extracellular filaments that are important for host interaction, yet their molecular identity remains unknown. Here, we applied single-particle cryo-electron microscopy to determine high-resolution structures of these filaments (2.8 and 3.6 [A]), enabling the unambiguous identification of two previously uncharacterized pilins from the experimental density maps. These pilins, designated PamA and PamB, assemble into unique helical filaments distinct from all previously characterized filaments in both domain architecture and assembly mechanism. Despite low sequence identity, both PamA and PamB share conserved structural principles, including Ig-like folds and donor-strand exchange-mediated assembly. Phylogenetic analysis indicates that Pam pilins are exclusive to CPR bacteria, with homologues distributed predominantly across the classes Saccharimonadia and Microgenomatia. Analysis of the conserved pam operon identifies putative chaperones (PamC and PamD) and assembly factors structurally homologous to chaperone-usher pili components, suggesting an analogous but distinct assembly pathway. These findings expand the known diversity of bacterial pilus systems and demonstrate the power of structural approaches for characterizing uncharacterized proteins encoded within CPR genomes.

microbiology↗

Efficacy of a bacteriophage cocktail targeting pathogenic bacteria associated with gastrointestinal dysfunction

The use of bacteriophage viruses that infect and kill bacteria is increasingly explored as an alternative to antibiotics for treatment of infections caused by opportunistic pathogens. Examples of opportunistic pathogens that disrupt the intestinal barrier and contribute to microbial imbalance in the gastrointestinal tract include Klebsiella pneumoniae, Pseudomonas aeruginosa and Serratia marcescens. This study evaluated the in vitro effectiveness of a bacteriophage cocktail composed of three host-specific phages: Lilla1 targeting Klebsiella pneumoniae, PAE1 targeting Pseudomonas aeruginosa and Smarc1 targeting Serratia marcescens. Bacterial growth was monitored by measuring optical density at 600 nm, and phage replication was quantified by plaque-forming unit assays. Each phage exhibited strong host specificity and produced significant reduction of growth of the corresponding bacterium while increasing in concentration during incubation. When applied as a cocktail, these three phages produced stronger and more sustained suppression of bacterial growth than single-phage treatments, both in individual cultures and in mixed cultures containing all three pathogens. In mixed cultures, continuous inhibition of bacterial growth persisted throughout a 24-hour incubation, and concentrations of Lilla1, PAE1 and Smarc1 increased significantly, indicating active replication and enhanced efficacy in combination. In single bacterial growth assays, bacterial populations that were initially suppressed showed regrowth after extended incubation. Regrowth manifested as a renewed increase in optical density several hours after initial decline and is consistent with selection of phage-resistant subpopulations, potentially arising from modification of surface receptors, phase variation or activation of adaptive defence systems. The observed biphasic response highlights the need for measures to limit microbial resistance to phage treatment, including expanded phage cocktails, adjusted dosing strategies and combined phage-antibiotic regimens. The results demonstrate that a three-phage cocktail can simultaneously inhibit multiple bacterial pathogens associated with gastrointestinal dysfunction and provide a basis for further in vivo evaluation and therapeutic development.

microbiology↗

Population-scale sequencing resolves correlates and determinants of latent Epstein-Barr Virus infection

Epstein-Barr Virus (EBV) is an endemic herpesvirus implicated in autoimmunity, cancer, and neurological disorders. Though primary infection typically resolves with subclinical symptoms, long-term complications can arise due to immune dysregulation or viral latency, in which EBV DNA is detectable in blood for decades. Despite the ubiquity of this virus, we have an incomplete understanding of the highly variable responses to EBV that range from asymptomatic infection to a trigger for severe disease. Here, we demonstrate that existing whole genome sequencing (WGS) data contains ample non-human DNA sequences to reconstruct a molecular biomarker of latent EBV infection consistent with orthogonal phenotypes, including viral serology. Using the UK Biobank (n = 490,560) and All of Us (n = 245,394), we uncover reproducible complex trait associations that nominate latent blood-derived EBV DNA as a respiratory, autoimmune, and cardiovascular disease biomarker. Further, we evaluate the genetic determinants of persistent EBV DNA via genome-wide and exome-wide association studies, uncovering protein-altering variants from 147 genes. Single-cell and pathway-scale enrichment analyses implicate variable antigen processing and presentation as a primary genetic determinant of latent EBV persistence, with gene programs expressed in B cells and antigen-presenting cells. Using predicted viral epitope presentation affinities, we implicate genetic variation in MHC class II as a key modulator of EBV DNA persistence. Our analyses demonstrate how existing WGS data can derive novel molecular biomarkers, which may generalize to dozens of viruses comprising the blood virome1.

genetics↗

Diverse ancestral representation improves genetic intolerance metrics

Rapidly expanding genomic databases have enabled the identification of regions in the human genome intolerant to variation and thus likely relevant to human disease. However, despite their unprecedented scale, these datasets remain constrained by limited ancestral diversity. Here, we systematically evaluate how genetic diversity impacts gene- and sub-genic intolerance metrics by analyzing whole-exome sequencing data from 460,551 UK Biobank participants and 125,748 gnomAD participants across diverse ancestral backgrounds. Through comprehensive analysis of randomly sampled datasets with varying ancestral compositions, we demonstrate that genetic diversity, rather than sample size alone, drives the performance of intolerance metrics in identifying functionally critical genes and genic sub-regions. Notably, scores trained on variation observed in African and Admixed American ancestral groups showed superior resolution in detecting neurodevelopmental disease risk genes and haploinsufficient genes compared to scores trained on variation observed in European ancestry cohorts. Most strikingly, the Missense Tolerance Ratio (MTR) trained on 43,000 multi-ancestry exomes demonstrated greater predictive power than when trained on a nearly 10-fold larger dataset of 440,000 non-Finnish European exomes, indicating that European ancestry-based scores are approaching saturation. These findings establish ancestral diversity as the fundamental determinant for advancing intolerance metrics and underscore the urgent scientific and ethical imperative for enhanced population representation in genomic resources to fully realize the potential of precision medicine and drug discovery.

genetics↗

Misexpression of inactive genes in whole blood is associated with nearby rare structural variants

Gene misexpression is the aberrant transcription of a gene in a context where it is usually inactive. Despite its known pathological consequences in specific rare diseases, we have a limited understanding of its wider prevalence and mechanisms in humans. To address this, we analyzed gene misexpression in 4,568 whole blood bulk RNA sequencing samples from INTERVAL study blood donors. We found that while individual misexpression events occur rarely, in aggregate they were found in almost all samples and over half of inactive genes. Using 2,821 paired whole genome and RNA sequencing samples, we identified that misexpression events are enriched in cis for rare structural variants. We established putative mechanisms through which a subset of SVs lead to gene misexpression, including transcriptional readthrough, transcript fusions and gene inversion. Overall, we develop misexpression as a novel type of transcriptomic outlier analysis and extend our understanding of the variety of mechanisms by which genetic variants can influence gene expression.

genetics↗

Codon affinity in mitochondrial DNA shapes evolutionary and somatic fitness

Summary ParagraphSomatic variation contributes to biological heterogeneity by modulating cellular proclivity to differentiate, expand, adapt, or die. While large-scale sequencing efforts have revealed the foundational role of somatic variants to drive human tumor evolution, our understanding of the contribution of mutations to modulate cellular fitness in non-malignant contexts remains understudied. Here, we identify a mosaic synonymous variant (m.7076A>G) in the mitochondrial DNA (mtDNA) encoded cytochrome c-oxidase subunit 1 gene (MT-CO1, p.Gly391=), which was present at homoplasmy in 47% of immune cells from a healthy donor. Using single-cell multi-omics, we discover highly specific selection against the m.7076G mutant allele in the CD8+ effector memory T cell compartment in vivo, reminiscent of selection observed for pathogenic mtDNA alleles1, 2 and indicative of lineage-specific metabolic requirements. While the wildtype m.7076A allele is translated via Watson-Crick-Franklin base-pairing, the anticodon diversity of the mitochondrial transfer RNA pool is limited, requiring wobble-dependent translation of the m.7076G mutant allele. Notably, mitochondrial ribosome profiling revealed altered codon-anticodon affinity at the wobble position as evidenced by stalled translation of the synonymous m.7076G mutant allele encoding for glycine. Generalizing this observation, we provide a new ontogeny of the 8,482 synonymous variants in the human mitochondrial genome that enables interpretation of functional mtDNA variation. Specifically, via inter- and intra-species evolutionary analyses, population-level complex trait associations, and the occurrence of germline and somatic mtDNA mutations from large-scale sequencing studies, we demonstrate that synonymous variation impacting codon:anticodon affinity is actively evolving across the entire mitochondrial genome and has broad functional and phenotypic effects. In summary, our results introduce a new ontogeny for mitochondrial genetic variation and support a model where organismal principles can be discerned from somatic evolution via single-cell genomics.

genetics↗

Genome-wide prediction of dominant and recessive neurodevelopmental disorder risk genes

Despite great progress in the identification of neurodevelopmental disorder (NDD) risk genes, there are thousands that remain to be discovered. Computational tools that provide accurate gene-level predictions of NDD risk can significantly reduce the costs and time needed to prioritize and discover novel NDD risk genes. Here, we first demonstrate that machine learning models trained solely on single-cell RNA-sequencing data from the developing human cortex can robustly predict genes implicated in autism spectrum disorder (ASD), developmental and epileptic encephalopathy (DEE), and developmental delay (DD). Strikingly, we find differences in gene expression patterns of genes with monoallelic and biallelic inheritance patterns. We then integrate these expression data with 300 orthogonal features in a semi-supervised machine learning framework (mantis-ml) to train inheritance-specific models for ASD, DEE, and DD. The models have high predictive power (AUCs: 0.84 to 0.95) and top-ranked genes were up to two-fold (monoallelic models) and six-fold (biallelic models) more enriched for high-confidence NDD risk genes than genic intolerance metrics. Across all models, genes in the top decile of predicted risk genes were 60 to 130 times more likely to have publications strongly linking them to the phenotype of interest in PubMed compared to the bottom decile. Collectively, this work provides highly robust novel NDD risk gene predictions that can complement large-scale gene discovery efforts and underscores the importance of incorporating inheritance into gene risk prediction tools (https://nddgenes.com).

genetics↗

Influences of rare protein-coding genetic variants on the human plasma proteome in 50,829 UK Biobank participants

Combining human genomics with proteomics is becoming a powerful tool for drug discovery. Associations between genetic variants and protein levels can uncover disease mechanisms, clinical biomarkers, and candidate drug targets. To date, most population-level proteogenomic studies have focused on common alleles through genome-wide association studies (GWAS). Here, we studied the contribution of rare protein-coding variants to 1,472 plasma proteins abundances measured via the Olink Explore 1536 assay in 50,829 UK Biobank human exomes. Through a variant-level exome-wide association study (ExWAS), we identified 3,674 rare and significant protein quantitative trait loci (pQTLs), of which 76% were undetected in a prior GWAS performed on the same cohort, and we found that rare pQTLs are less likely to be random in their variant effect annotation. In gene-based collapsing analyses, we identified an additional 166 significant gene-protein pQTL signals that were undetected through single-variant analyses. Of the total 456 protein-truncating variant (PTV)-driven cis-pQTLs in the gene-based collapsing analysis, 99.3% were associated with decreased protein levels. We demonstrate how this resource can identify allelic series and propose biomarkers for several candidate therapeutic targets, including GRN, HSD17B13, NLRC4, and others. Finally, we introduce a new collapsing analysis framework that combines PTVs with missense cis-pQTLs that are associated with decreased protein abundance to bolster genetic discovery statistical power. Our results collectively highlight a considerable role for rare variation in plasma protein abundance and demonstrate the utility of plasma proteomics in gene discovery and unravelling mechanisms of action.

genomics↗

A minimal role for synonymous variation in human disease

Synonymous mutations change the DNA sequence of a gene without affecting the amino acid sequence of the encoded protein. Although emerging evidence suggests that synonymous mutations can impact RNA splicing, translational efficiency, and mRNA stability1, studies in human genetics, mutagenesis screens, and other experiments and evolutionary analyses have repeatedly shown that most synonymous variants are neutral or only weakly deleterious, with some notable exceptions. In their recent article, Shen et al. claim to have disproved these well-established findings. They perform mutagenesis experiments in yeast and conclude that synonymous mutations frequently reduce fitness to the same extent as nonsynonymous mutations2. Based on their findings, the authors state that their results "imply that synonymous mutations are nearly as important as nonsynonymous mutations in causing disease." An accompanying News and Views argues that "revising our expectations about synonymous mutations should expand our view of the genetic underpinnings of human health"3. Considering potential technical concerns with these experiments4 and a large, coherent body of knowledge establishing the predominant neutrality of synonymous variants, we caution against interpreting this study in the context of human disease.

genetics↗

Genotyping, sequencing and analysis of 140,000 adults from the Mexico City Prospective Study

The Mexico City Prospective Study (MCPS) is a prospective cohort of over 150,000 adults recruited two decades ago from the urban districts of Coyoacan and Iztapalapa in Mexico City. We generated genotype and exome sequencing data for all individuals, and whole genome sequencing for 10,000 selected individuals. We uncovered high levels of relatedness and substantial heterogeneity in ancestry composition across individuals. Most sequenced individuals had admixed Native American, European and African ancestry, with extensive admixture from indigenous groups in Central, Southern and South Eastern Mexico. Native Mexican segments of the genome had lower levels of coding variation, but an excess of homozygous loss of function variants compared with segments of African and European origin. We estimated population specific allele frequencies at 142 million genomic variants, with an effective sample size of 91,856 for Native Mexico at exome variants, all available via a public browser. Using whole genome sequencing, we developed an imputation reference panel which outperforms existing panels at common variants in individuals with high proportions of Central, South and South Eastern Native Mexican ancestry. Our work illustrates the value of genetic studies in populations with diverse ancestry and provides foundational imputation and allele frequency resources for future genetic studies in Mexico and in the United States where the Hispanic/Latino population is predominantly of Mexican descent.

genetics↗

Cancer-driving mutations are enriched in genic regions intolerant to germline variation

Large reference datasets of protein-coding variation in human populations have allowed us to determine which genes and genic sub-regions are intolerant to germline genetic variation. There is also a growing number of genes implicated in severe Mendelian diseases that overlap with genes implicated in cancer. Here, we hypothesized that mitotically mutable genic sub-regions that are intolerant to germline variation are enriched for cancer-driving mutations. We introduce a new metric, OncMTR, which uses 125,748 exomes in the gnomAD database to identify genic sub-regions intolerant to germline variation but enriched for hematologic somatic variants. We demonstrate that OncMTR can significantly predict driver mutations implicated in hematologic malignancies. Divergent OncMTR regions were enriched for cancer-relevant protein domains, and overlaying OncMTR scores on protein structures identified functionally important protein residues. Finally, we performed a rare variant, gene-based collapsing analysis on an independent set of 394,694 exomes from the UK Biobank and find that OncMTR dramatically improves genetic signals for hematologic malignancies. Our web app enables easy visualization of OncMTR scores for each protein-coding gene (https://astrazeneca-cgr-publications.github.io/OncMTR-Viewer/).

genomics↗

Surveying the contribution of rare variants to the genetic architecture of human disease through exome sequencing of 177,882 UK Biobank participants

The UK Biobank (UKB) represents an unprecedented population-based study of 502,543 participants with detailed phenotypic data and linkage to medical records. While the release of genotyping array data for this cohort has bolstered genomic discovery for common variants, the contribution of rare variants to this broad phenotype collection remains relatively unknown. Here, we use exome sequencing data from 177,882 UKB participants to evaluate the association between rare protein-coding variants with 10,533 binary and 1,419 quantitative phenotypes. We performed both a variant-level phenome-wide association study (PheWAS) and a gene-level collapsing analysis-based PheWAS tailored to detecting the aggregate contribution of rare variants. The latter revealed 911 statistically significant gene-phenotype relationships, with a median odds ratio of 15.7 for binary traits. Among the binary trait associations identified using collapsing analysis, 83% were undetectable using single variant association tests, emphasizing the power of collapsing analysis to detect signal in the setting of high allelic heterogeneity. As a whole, these genotype-phenotype associations were significantly enriched for loss-of-function mediated traits and currently approved drug targets. Using these results, we summarise the contribution of rare variants to common diseases in the context of the UKB phenome and provide an example of how novel gene-phenotype associations can aid in therapeutic target prioritisation.

genomics↗

A broad exome study of the genetic architecture of asthma reveals novel patient subgroups

IntroductionAsthma risk is a complex interplay between genetic susceptibility and environment. Despite many significantly-associated common variants, the contribution of rarer variants with potentially greater effect sizes has not been as extensively studied. We present an exome-based study adopting 24,576 cases and 120,530 controls to assess the contribution of rare protein-coding variants to the risk of early-onset or all-comer asthma. MethodsWe performed case-control analyses on three genetic units: variant-, gene- and pathway-level, using sequence data from the Scandinavian Asthma Genetic Study and UK Biobank participants with asthma. Cases were defined as all-comer asthma (n=24,576) and early-onset asthma (n=5,962). Controls were 120,530 UK Biobank participants without reported history of respiratory illness. ResultsVariant-level analyses identified statistically significant variants at moderate-to-common allele frequency, including protein-truncating variants in FLG and IL33. Asthma risk was significantly increased not only by individual, common FLG protein-truncating variants, but also among the collection of rare-to-private FLG protein-truncating variants (p=6.8x10-7). This signal was driven by early-onset asthma and did not correlate with circulating eosinophil levels. In contrast, a single splice variant in IL33 was significantly protective (p=8.0x10-10), while the collection of remaining IL33 protein-truncating variants showed no class effect (p=0.54). A pathway-based analysis identified that protein-truncating variants in loss-of-function intolerant genes were significantly enriched among individuals with asthma. ConclusionsAccess to the full allele frequency spectrum of protein-coding variants provides additional clarity about the potential mechanisms of action for FLG and IL33. Beyond these two significant drivers, we detected a significant enrichment of protein-truncating variants in loss-of-function intolerant genes.

genomics↗

Human essentiality genes and targeted oncology therapies

Human essentiality genes are significantly enriched in targeted therapies successfully used in oncology. Embedding human essentiality metrics into discovery pipelines could optimise the delivery of highly effective targeted therapies among clinical development strategies.

genomics↗

Identification of a novel missense variant in SPDL1 associated with idiopathic pulmonary fibrosis

Idiopathic pulmonary fibrosis (IPF) is a fatal disorder characterised by progressive, destructive lung scarring. Despite significant progress, the genetic determinants of this disease remain incompletely defined. Using next generation sequencing data from 752 individuals with sporadic IPF and 119,055 controls, we performed both variant- and gene-level analyses to identify novel IPF genetic risk factors. Our variant-level analysis revealed a novel rare missense variant in SPDL1 (NM_017785.5 p.Arg20Gln; p = 2.4 x 10-7, odds ratio = 2.87). This signal was independently replicated in the FinnGen cohort (combined p = 2.2 x 10-20), firmly associating this variant as a novel IPF risk allele. SPDL1 encodes Spindly, a protein involved in mitotic checkpoint signalling during cell division that has not been previously described in fibrosis. Our results highlight a novel mechanism underlying IPF, providing the potential for new therapeutic discoveries in a disease of great unmet need.

genetics↗

Systematic re-annotation of 191 genes associated with early-onset epilepsy unmasks de novo variants linked to Dravet syndrome in novel SCN1A exons

The early infantile epileptic encephalopathies (EIEE) are a group of rare, severe neurodevelopmental disorders, where even the most thorough sequencing studies leave 60-65% of patients without a molecular diagnosis. Here, we explore the incompleteness of transcript models used for exome and genome analysis as one potential explanation for lack of current diagnoses. Therefore, we have updated the GENCODE gene annotation for 191 epilepsy-associated genes, using human brain-derived transcriptomic libraries and other data to build 3,550 novel putative transcript models. The extended transcriptional footprint of these genes allowed for 294 intronic or intergenic variants, found in human mutation databases, to be reclassified as exonic, while a further 70 intronic variants were reclassified as splice-site proximal. Using SCN1A as a case study due to its close phenotype/genotype correlation with Dravet syndrome, we screened 122 people with Dravet syndrome, or a similar phenotype, with a panel of novel exon sequences representing eight established genes and identified two de novo SCN1A variants that now, through improved gene annotation can be ascribed to residing among novel exons. These two (from 122 screened patients, 1.6%) new molecular diagnoses carry significant clinical implications. Furthermore, we identified a previously-classified SCN1A intronic Dravet-associated variant that now lies within a deeply conserved novel exon. Our findings illustrate the potential gains of thorough gene annotation in improving diagnostic yields for genetic disorders. We would expect to find new molecular diagnoses in our 191 genes that were originally suspected by clinicians for patients, with a negative diagnosis.

genomics↗

Stochastic semi-supervised learning to prioritise genes from high-throughput genomic screens

Access to large-scale genomics datasets has increased the utility of hypothesis-free genome-wide analyses that result in candidate lists of genes. Often these analyses highlight several gene signals that might contribute to pathogenesis but are insufficiently powered to reach experiment-wide significance. This often triggers a process of laborious evaluation of highly-ranked genes through manual inspection of various public knowledge resources to triage those considered sufficiently interesting for deeper investigation. Here, we introduce a novel multi-dimensional, multi-step machine learning framework to objectively and more holistically assess biological relevance of genes to disease studies, by relying on a plethora of gene-associated annotations. We developed mantis-ml to serve as an automated machine learning (AutoML) framework, following a stochastic semi-supervised learning approach to rank known and novel disease-associated genes through iterative training and prediction sessions of random balanced datasets across the protein-coding exome (n=18,626 genes). We applied this framework on a range of disease-specific areas and as a generic disease likelihood estimator, achieving an average Area Under Curve (AUC) prediction performance of 0.85. Critically, to demonstrate applied utility on exome-wide association studies, we overlapped mantis-ml disease-specific predictions with data from published cohort-level association studies. We retrieved statistically significant enrichment of high mantis-ml predictions among the top-ranked genes from hypothesis-free cohort-level statistics (p<0.05), suggesting the capture of true prioritisation signals. We believe that mantis-ml is a novel easy-to-use tool to support objectively triaging gene discovery and overall enhancing our understanding of complex genotype-phenotype associations.

bioinformatics↗