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Guerra-Assuncao, J. A.

Publications and source records attributed to Guerra-Assuncao, J. A..

11 recordsLinked to original sources

Mitochondrial dsRNA from B-ALL cells stimulates mesenchymal stromal cells to become cancer associated fibroblasts

Cancer associated fibroblasts (CAF) arising from bone marrow-derived mesenchymal stromal cells (MSC) are prominent in B-precursor acute lymphoblastic leukaemia (B-ALL). We have previously shown that CAF formation is triggered by exposure to reactive oxygen species-inducing chemotherapy and that CAF support chemoresistance by donating mitochondria to the cancer cells, through tunnelling nanotubes. In the present study, we show that exposure of MSC to ALL cell lines, PDX and primary cells or their conditioned media can also trigger CAF formation, in an oncogene-dependent manner. Using bulk RNA sequencing in cell lines, we show that the MSC to CAF transition is accompanied by a robust interferon pathway response and we have validated this finding in primary cells. Using confocal microscopy and flow cytometry, we identify the take up of leukaemia cell-derived mitochondrial dsRNA by MSC as a proximate trigger for the MSC to CAF transition. We show that degradation of dsRNA in ALL cell conditioned media by DMSO ablates the ability of the conditioned media to stimulate MSC to CAF transition. Since we find that only specific primary driver genetic subtypes of B-ALL possess the property to directly generate CAFs, we propose this phenomenon as the first mechanistic insight into the strong relationship between acute lymphoblastic leukaemia genetic subtype and survival outcomes. Key pointsX Exposure of MSC to B-precursor ALL cell lines triggers cancer-associated fibroblast formation in an oncogene-dependent manner The proximate trigger for CAF formation is ALL-derived mitochondrial double stranded RNA

cancer biology↗

Essential role of proline synthesis and the one-carbon metabolism pathways for systemic virulence of Streptococcus pneumoniae

Previous virulence screens have indicated potential roles during Streptococcus pneumoniae infection for the one-carbon metabolism pathway component Fhs and proline synthesis mediated by ProABC. To define how these metabolic pathways affect S. pneumoniae virulence we have investigated phenotypes and transcription profiles of {Delta}fhs and {Delta}proABC strain mutants. S. pneumoniae capsular serotype 6B BHN418 {Delta}fhs and {Delta}proABC mutant strains were markedly reduced virulence in mouse models of systemic infection and pneumonia, but were still able to colonise the nasopharynx. Although the {Delta}fhs and {Delta}proABC mutant strains grew normally in complete media, both mutant strains had markedly impaired growth in chemically defined medium, human serum and human CSF. The {Delta}proABC strain also had impaired growth under conditions of osmotic and oxidative stress. When transferred to the serotype 2 D39 S. pneumoniae strain background, the {Delta}fhs mutation replicated the virulence and growth in serum phenotype of the BHN418 mutation. In contrast, the D39 {Delta}proABC mutant could cause septicaemia and grow in human serum, indicating the role of this genetic locus during virulence is strain-specific. In human sera the {Delta}fhs and {Delta}proABC mutants both had major derangements in global gene transcription affecting multiple but different metabolic pathways, identifying the corresponding S. pneumoniae metabolic functions affected by these genes under infection-related conditions. Our data demonstrate an essential role for the S. pneumoniae one- carbon metabolism and a strain-conditional role for proline biosynthesis for growth in physiological fluids and therefore systemic infection, and further demonstrate the vital importance of bacterial metabolism for disease pathogenesis. ImportanceRapid adaptation to grow within the physiological conditions found in the host environment is an essential but poorly understood virulence requirement for systemic pathogens such as Streptococcus pneumoniae. We have now demonstrated an essential role for the one-carbon metabolism pathway and a conditional role depending on strain background for proline biosynthesis for S. pneumoniae growth in serum or CSF and therefore for systemic virulence. RNAseq data demonstrated that loss of one carbon metabolism or proline biosynthesis both have profound but differing effects on S. pneumoniae metabolism in human serum, identifying the metabolic processes dependent on each pathway during systemic infection. These data provide a more detailed understanding of the adaptations required by systemic bacterial pathogens in order to cause infection, and demonstrate that the requirement for some of these adaptations vary between strains from the same species and could therefore underpin strain variations in virulence potential.

microbiology↗

Impact of Streptococcus pneumoniae biosynthesis gene mutations on epithelial microinvasion and cellular responses

Nasopharyngeal colonisation by Streptococcus pneumoniae is characterised by bacterial adherence to epithelial cells, microinvasion and innate immune activation. Previously, we have shown two serotype 6B S. pneumoniae mutant strains affecting bacterial metabolism ({Delta}proABC/pia and{Delta} fhs/pia) colonise humans and mice, but in a murine disease model do not cause invasive infection. Here, we explore whether S. pneumoniae epithelial microinvasion and the induction of innate immune responses persist despite disease attenuation. We show that under serum stress, these biosynthesis gene mutations had a broad but different impact on pneumococcal virulence gene expression, oxidative stress regulation, and purine and carbohydrate metabolism genes. However, although these mutations did not attenuate microinvasion in human challenge and epithelial models, there was less transmigration of Detroit 562 nasopharyngeal epithelial cells by the mutants compared to WT. Cellular reorganisation of primary human airway epithelium varied considerably between strains. Compared to WT, infection of Detroit 562 epithelial cells by the{Delta} fhs/piaA strain, but not the{Delta} proABC/piaA strain was less pro-inflammatory, induced less caspase 8 production, and were associated with increased pneumococcal hydrogen peroxide and reduced pneumolysin secretion. These findings suggest that the observed differences in microinvasion and the epithelial response were driven by the differential expression of multiple bacterial virulence and metabolic pathways, rather than single genes or pathways of genes. These data highlight the complex impact of single gene mutations on bacterial virulence and suggest that the virulence determinants of pneumococcal epithelial colonisation, microinvasion and innate immunity are not necessarily directly linked to disease. Author SummaryStreptococcus pneumoniae (the pneumococcus) commonly colonises the back of the human nose, and is a leading cause of pneumonia, meningitis, and sepsis. During colonisation, the pneumococcus adheres to the cells in the nose, invades these cells (so-called microinvasion), and activates them. Colonisation is a pre-requisite for disease, however, since disease is largely a dead end for S. pneumoniae, it remains unclear whether these processes are directly linked to disease progression. We have previously shown that if we introduce gene mutations into S. pneumoniae that affect key metabolic pathways, these bacteria retain their ability to colonize human and animal models without causing disease. We now show that these mutants retain their ability to microinvade epithelial cells in human and mouse models, and some may still cause inflammation, but are less able to pass through the epithelial barrier. However, although the attenuation of disease may be explained by the broad-ranging impact of these mutations on pneumococcal virulence, oxidative stress, and metabolism, they are not driven by a single determinant. Our findings suggest that pneumococcal microinvasion and immune activation are not necessarily pre-cursors to disease progression. This supports the idea that S. pneumoniae adapts and evolves to promote colonisation and ultimately transmission rather than cause disease. Graphical AbstractS. pneumoniae colonisation is characterised by mucus association, epithelial adherence, microcolony formation and microinvasion - where the pneumococcus invades the epithelial barrier without causing disease. Although mutations in S. pneumoniae biosynthesis genes ({Delta}proABC and{Delta} fhs) attenuate disease in a murine model, they do not attenuate microinvasion in either experimental human pneumococcal challenge (EHPC), ex vivo or in vitro epithelial cells. Transmigration of the epithelial barrier is attenuated. These mutations show strain-dependent effects on both the epithelial and bacterial responses to infection. Factors such as epithelial cellular reorganisation, inflammation and caspase 8 activity alongside pneumococcal metabolic adaptation, virulence factor expression and response to stress are important components of these processes. O_FIG O_LINKSMALLFIG WIDTH=200 HEIGHT=86 SRC="FIGDIR/small/545009v8_ufig1.gif" ALT="Figure 1"> View larger version (24K): org.highwire.dtl.DTLVardef@11a17aeorg.highwire.dtl.DTLVardef@8c707org.highwire.dtl.DTLVardef@42abf8org.highwire.dtl.DTLVardef@12850f9_HPS_FORMAT_FIGEXP M_FIG C_FIG

microbiology↗

Genetic consequences of effective and suboptimal dosing with mutagenic drugs in a hamster model of SARS-CoV-2 infection

Mutagenic antiviral drugs have shown promising results against multiple viruses, yet concerns have been raised about whether their use might promote the emergence of new and harmful viral variants. Here, we examine the genetic consequences of effective and suboptimal dosing of favipiravir and molnupiravir in the treatment of SARS-CoV-2 infection in a hamster model. We identify a dose-dependent effect upon the mutational load in a viral population, with molnupiravir having a greater potency than favipiravir per mg/kg of treatment. The emergence of de novo variants was largely driven by stochastic processes, with evidence of compensatory adaptation but not of the emergence of drug resistance or novel immune phenotypes. Effective doses for favipiravir and molunpiravir correspond to similar levels of mutational load. Combining both drugs had an increased impact on both efficacy and mutational load. Our results suggest the potential for mutational load to provide a marker for clinical efficacy.

evolutionary biology↗

AYUKA: A toolkit for fast viral genotyping using whole genome sequencing.

Technological advances enabled the frequent use of whole genome sequencing in the clinical microbiology laboratory. While generating data is now easier than ever, the computational resources and expertise required for analysis are still a challenge for clinical applications. Since it is not always possible to collect clinical specimens at the peak viral load, sequencing results are also not always amenable for analysis with bioinformatics pipelines that always require high quality data. Here we present a fast and reliable method, we named AYUKA, for analysis of viral sequencing data that does not require data pre-processing and provides quality control metrics including estimates for sequencing depth and genome coverage, as well as identifying the viral genotypes in a sample and distinguishing mixed infection from recombinants. This method can be applied to any virus where a classification by genotype is employed and determining it is relevant. We generated a validation dataset composed of cultured and sequenced reference adenoviruses from distinct species, that we compared with the gold standard clinical processing pipeline currently implemented to demonstrate reliability. The validation shows better sensitivity than mapping and perfect specificity in detecting the correct genotypes and in a wide range of adenovirus species. Run time was consistently under one minute per sample on a standard laptop, allowing the analysis of more than 100 samples per hour. This open-source method is available at https://github.com/afonsoguerra/AYUKA and precomputed databases are available at https://zenodo.org/record/6521576 allowing analysis of raw data straight from the sequencer within minutes on a standard computer, with minimum setup or expertise required to perform the analysis. The information contained within the AYUKA report can be of use for both the clinical team that collected the sample, but also for guiding the bioinformatics analysis team in the in-depth downstream analyses and genetic epidemiology investigations.

bioinformatics↗

HIV-1 Vpr drives a tissue residency-like phenotype during selective infection of resting memory T cells

Human immunodeficiency virus type 1 (HIV-1) replicates in CD4+ T cells leading to profound T cell loss, immunological dysfunction and AIDS. Determining how HIV-1 shapes the immunological niche in which it resides to create a permissive environment is central to informing efforts to limit pathogenesis, disturb viral reservoirs and achieve a cure. A key roadblock in understanding HIV-T cell interactions is the requirement to activate CD4+ T cells in vitro in order to make them permissive to infection. This dramatically alters T cell biology, obscuring native virus-host interactions. Here we show that HIV-1 cell-to-cell spread permits efficient and productive infection of resting CD4+ T cells without the need for prior activation. Infection is preferential for resting memory T cells, is observed with both CXCR4-tropic virus and CCR5-tropic transmitter-founder viruses and results in virus production and onward spreading infection. Strikingly, we find that HIV-1 infection of resting memory CD4+ T cells primes for induction of a tissue-resident memory (TRM)-like phenotype evidenced by upregulation of TRM markers CD69/CXCR6 alongside co-expression of CD49a, PD-1, CD101 as well as transcription factor Blimp-1. Furthermore, we reveal that HIV-1 initiates a transcriptional program that overlaps with the core TRM transcriptional signature. This reprograming depends on the HIV-1 accessory protein Vpr. We propose that HIV-1 infection drives a CD4+ TRM-phenotype potentially sequestering infected cells within tissues to support viral replication and persistence.

microbiology↗

GenomeChronicler: The Personal Genome Project UK Genomic Report Generator Pipeline

In recent years, there has been a significant increase in whole genome sequencing data of individual genomes produced by research projects as well as direct to consumer service providers. While many of these sources provide their users with an interpretation of the data, there is a lack of free, open tools for generating reports exploring the data in an easy to understand manner. GenomeChronicler was developed as part of the Personal Genome Project UK (PGP-UK) to address this need. PGP-UK provides genomic, transcriptomic, epigenomic and self-reported phenotypic data under an open-access model with full ethical approval. As a result, the reports generated by GenomeChronicler are intended for research purposes only and include information relating to potentially beneficial and potentially harmful variants, but without clinical curation. GenomeChronicler can be used with data from whole genome or whole exome sequencing, producing a genome report containing information on variant statistics, ancestry and known associated phenotypic traits. Example reports are available from the PGP-UK data page (personalgenomes.org.uk/data). The objective of this method is to leverage existing resources to find known phenotypes associated with the genotypes detected in each sample. The provided trait data is based primarily upon information available in SNPedia, but also collates data from ClinVar, GETevidence and gnomAD to provide additional details on potential health implications, presence of genotype in other PGP participants and population frequency of each genotype. The analysis can be run in a self-contained environment without requiring internet access, making it a good choice for cases where privacy is essential or desired: any third party project can embed GenomeChronicler within their off-line safe-haven environments. GenomeChronicler can be run for one sample at a time, or in parallel making use of the Nextflow workflow manager. The source code is available from GitHub (https://github.com/PGP-UK/GenomeChronicler), container recipes are available for Docker and Singularity, as well as a pre-built container from SingularityHub (https://singularity-hub.org/collections/3664) enabling easy deployment in a variety of settings. Users without access to computational resources to run GenomeChronicler can access the software from the Lifebit CloudOS platform (https://lifebit.ai/cloudos) enabling the production of reports and variant calls from raw sequencing data in a scalable fashion.

bioinformatics↗

The Personal Genome Project-UK: an open access resource of human multi-omics data

Integrative analysis of multi-omics data is a powerful approach for gaining functional insights into biological and medical processes. Conducting these multifaceted analyses on human samples is often complicated by the fact that the raw sequencing output is rarely available under open access. The Personal Genome Project UK (PGP-UK) is one of few resources that recruits its participants under open consent and makes the resulting multi-omics data freely and openly available. As part of this resource, we describe the PGP-UK multi-omics reference panel consisting of ten genomic, methylomic and transcriptomic data. Specifically, we outline the data processing, quality control and validation procedures which were implemented to ensure data integrity and exclude sample mix-ups. In addition, we provide a REST API to facilitate the download of the entire PGP-UK dataset. The data are also available from two cloud-based environments, providing platforms for free integrated analysis. In conclusion, the genotype-validated PGP-UK multi-omics human reference panel described here provides a valuable new open access resource for integrated analyses in support of personal and medical genomics.

bioinformatics↗

Both the inflammatory response and clinical outcome differ markedly between adults with pneumococcal and meningococcal meningitis in a high HIV-1 prevalent setting in sub-Saharan Africa

Outcomes from pneumococcal meningitis (PM) are worse than meningococcal meningitis (MM), particularly in settings with high HIV-1 prevalence, but the reasons are unknown. We compared inflammatory responses between PM and MM in Malawian adults. As compared to MM (n=27, 67% HIV-infected, mortality 11%), patients with PM (n=440, 84% HIV-infected, mortality 54%) were older, had strikingly lower CSF WCC, higher pro-inflammatory cytokine concentrations and higher mortality. PM is characterized by significantly lower CSF WCC, but greater inflammation and higher mortality compared to MM. Mechanistic understanding of blunting of the CSF leukocyte response in PM in-vivo is required.

immunology↗

Cerebrospinal fluid transcriptional analyses reveals upregulation of IL-17, Type 1 interferon transcriptional pathways and neutrophil persistence genes associated with increased mortality from pneumococcal meningitis in adults

BackgroundImproving outcomes from pneumococcal meningitis (PM), particularly in populations with high HIV prevalence, requires better understanding of host inflammatory responses to infection.\n\nMethodsWe compared the transcriptome in pre-antibiotic cerebrospinal fluid (CSF) and blood from Malawian adults with PM using RNA sequencing. We used network analyses and cellular/process deconvolution of the transcriptome to identify important patho-physiological associations with outcome.\n\nFindingsBlood transcriptional profiles were obtained in 28 patients (21 HIV co-infected; median age 33 years [26-66]; median CSF WCC 28 cells/mm3 [0-3660]; median bacterial load 4.7x106 copies/ml CSF [671-2x109]; in-hospital mortality 64%), paired CSF profiles were obtained in 13. Marked differences in gene expression by outcome were confined to the CSF. In non-survivors, differentially expressed genes in the CSF were co-correlated in a network of pro-inflammatory gene-clusters enriched for collagen degradation and platelet degranulation. In contrast, CSF gene expression networks from surviving patients were dominated by DNA repair, transcriptional regulation and immunological signalling. CSF expression of gene response-modules for IL-17, Type 1 interferons and IL-10 were enriched in non-survivors, expression of cell-specific response-modules did not differ by outcome. However, genes for neutrophil chemotaxis and persistence were highly over-expressed in non-survivors.\n\nInterpretationThese data suggest poor outcome in PM is associated with over-expression of IL-17 and T1-IFN associated pro-inflammatory responses in the CSF and suggest a role for neutrophil-mediated inflammation. These responses are unlikely to be effected by current adjunctive treatments. Improving poor outcomes from PM will require better-targeted interventions.\n\nFundingAcademy of Medical Sciences (UK), Wellcome Trust (UK) (089671/B/09/Z)

immunology↗

PGP-UK: a research and citizen science hybrid project in support of personalized medicine

Molecular analyses such as whole-genome sequencing have become routine and are expected to be transformational for future healthcare and lifestyle decisions. Population-wide implementation of such analyses is, however, not without challenges, and multiple studies are ongoing to identify what these are and explore how they can be addressed. Defined as a research project, the Personal Genome Project UK (PGP-UK) is part of the global PGP network and focuses on open data sharing and citizen science to advance and accelerate personalized genomics and medicine. Here we report our findings on using an open consent recruitment protocol, active participant involvement, open access release of personal genome, methylome and transcriptome data and associated analyses, including 47 new variants predicted to affect gene function and innovative reports based on the analysis of genetic and epigenetic variants. For this pilot study, we recruited ten participants willing to actively engage as citizen scientists with the project. In addition, we introduce Genome Donation as a novel mechanism for openly sharing previously restricted data and discuss the first three donations received. Lastly, we present GenoME, a free, open-source educational app suitable for the lay public to allow exploration of personal genomes. Our findings demonstrate that citizen science-based approaches like PGP-UK have an important role to play in the public awareness, acceptance and implementation of genomics and personalized medicine.

genomics↗