Browsing by Author "Lynch, Tarah"

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    Biological insights into the parasitic nematode Heligmosomoides bakeri from bulk and single-cell transcriptomics
    (2023-12-05) Pollo, Stephen Michael Jerome; Wasmuth, James; Gilleard, John; Lynch, Tarah; Niu, Dongyan
    Heligmosomoides bakeri, a parasitic nematode (roundworm) of mice, is closely related to economically important parasites of livestock and the hookworm parasites of humans. As a murine parasite it is more amenable to being maintained and manipulated in a controlled laboratory environment than its relatives. The worm enters its host during its third larval stage and develops through another larval stage into adults that reside in the lumen of the small intestine to mate and lay their eggs. Unravelling these processes and other processes critical to H. bakeri survival could reveal new targets to use for drug discovery for controlling this group of parasites as well as refine previous predictions of immunomodulatory molecules, which have therapeutic potential. My thesis aims to describe the gene expression of H. bakeri during the parasitic phase of its lifecycle. I first used RNA sequencing to investigate how the (whole worm) expression of genes varies across the parasite’s infection. Using differential gene expression analyses I identified genes important for development and genes important for the males vs the females. I also uncovered evidence of an increased importance for anaerobic respiration in the adults compared to the larvae and hypothesize that aerobic conditions are important for the critical developmental processes of molting and cuticle synthesis. I then analyzed single-cell RNA-seq data from young adult male and female worms. Leveraging cell type markers from the model nematode C. elegans allowed me to putatively identify gamete, embryo, intestine, hypodermis, neuron, and muscle cells. The resulting cluster expression profiles can guide investigations into tissue-specific aspects of the adult worms. Putative intestinal transcription profiles suggest compartmentalization of function along the anterior-posterior axis of the worms, with an emphasis on protein synthesis in the anterior portion, as has been observed in other worms. Embryonic profiles are noticeably different from C. elegans embryogenesis, particularly with respect to paternal contributions to the early embryo. Overall, these datasets extend our understanding of how H. bakeri lives as a parasite and provide a public resource for further investigation into genes of interest. They also lay the groundwork for more comprehensive comparisons among the phylum Nematoda.
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    Endocarditis caused by an oral taxon species of Bergeyella identified by partial 16S rDNA sequencing: case report and review of the literature
    (University of Toronto Press, 2017) Clark, Lauren; Parkins, Michael D; Chow, Barbara L; Lynch, Tarah; Church, Deirdre
    Bergeyella spp bacteremia is a rare cause of infective endocarditis and is typically associated with animal contact. This case report presents a case of culture-negative endocarditis caused by Bergeyella spp oral taxon 422 in a 49-year-old man with severe periodontal disease but no animal contact. Multiple sets of blood cultures were negative, but broad-range 16S rDNA polymerase chain reaction (PCR) amplification and sequencing repeatedly detected this organism in the patient’s bloodstream. Empiric broad-spectrum antibiotic treatment against Bergeyella spp resulted in resolution of clinical symptoms, resolution of bloodstream infection, and cure. This is the first human case of endocarditis caused by an oral-associated species of Bergeyella described in the literature. Culture-negative endocarditis due to Bergeyella spp from severe periodontal disease may be missed unless molecular detection methods are used.
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    Identification of Somatic Mutational Patterns with Biological and Clinical Significance in Solid and Hematological Malignancies
    (2024-01-17) McNeil, Reid Evan; Bose, Pinaki; Khan, Faisal; Storek, Jan; Lynch, Tarah
    Cancers use Darwinian evolution to naturally select for advantageous DNA alterations that allow these malignancies to escape normal biological control mechanisms. Advantageous alterations are known as driver mutations that modify cellular phenotype causing cancer cells to proliferate, invade adjacent tissues, and metastasize to other organs. Even across very different types of cancers, DNA alteration events are an underlying commonality. Using DNA alterations as a lens to analyze cancers can potentially identify cross cancer biomarkers implicated in disease development, progression, prognostication, and therapeutic drug targeting and response. In this MSc thesis, we hypothesis that in squamous cell carcinomas a subtype of alteration called DNA amplification events can modulate tumor biology through gene expression, and that point mutations in myeloid malignancies can predict clinical outcomes like disease relapse after bone marrow transplant. Aim one of my thesis investigated DNA amplifications to identify how they modulate mRNA and protein expression in head and neck and lung SCCs. Using genomic, transcriptomic, and proteomics data we identify amplification driven expression programs with biological and clinical significance in SCCs. Aim two of my thesis investigated point mutation profiles of myeloid malignancies using the Illumina TruSight Tumor (TST) Myeloid sequencing panel and machine learning analysis. Mutational landscape analysis of all myeloid samples annotated for DNA mutations of clinical relevance. Machine learning analysis was used point mutation profiles to predict relapse status of patients after transplant. The main research findings indicated that in SCCs, the 3q22-29 and 11q13 DNA amplifications were the top events in HNSCs and LUSCs. Several genes from 3q22-29 (ABCC5, ALG3, FXR1, TFRC, and RFC4) and 11q13 amplified regions (CTTN, FADD, and PPFIA1) were overexpressed on the mRNA and protein level. These genes were majority expressed in tumoral tissue and cancerous cells, and when overexpressed led to worse patient survival. The 3q22-29 amplified samples were negatively correlated with immune related pathways in the tumor microenvironment. Specifically, TRAIL and IFNG signaling levels were lower in 3q22-29 amplified samples, along with lower levels of immune cell infiltration of natural killer and cytotoxic cells. In myeloid malignancies, point mutations of clinical significance were identified, the most common mutations across 545 AML samples were TET2, ASXL1, and DNMT3A. The TET2 gene modulates DNA methylation levels and mutations to this gene trigger malignant transformation of myeloid progenitor cells and development of cancer. Patients with TET2 mutations can be treated with azacitidine in combination with chemotherapies to increase overall patient survival. The machine learning analysis of mutation profiles of myeloid patients who went through a bone marrow transplant were able to predict relapse status of patients from mutations profiles generated at disease diagnosis. The random forest model was the best performing model (AUC = 0.845) to predict relapse status after transplantation. Altogether, this analysis demonstrated the ability and importance DNA alterations have in diseases like cancer.
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    The impact of transposable elements on genomes of parasitic nematodes
    (2020-07-06) Dunemann, Sonja Maria; Wasmuth, James D.; Lynch, Tarah; Deardon, Rob; Yeaman, Sam
    Parasitic nematodes infect many animal and plant species. In humans, they cause significant levels of morbidity and death in low and middle income countries. In livestock and crop plants, they have a significant, negative economic impact, globally. To better understand the biology of these organisms, we must understand their genetic makeup. Up to 36% of parasitic nematode genomes consist of transposable elements (TEs). TEs are mobile, repetitive elements, and act as major players of evolution due to their ability to transfer horizontally between different taxa, move within genomes, and impact the phenotype of their host. However, TEs are often sidelined in standard genomic and transcriptomic analyses. Hence, we know little about their impact on and interaction with nematodes. Here I show that TEs can be horizontally transferred between parasitic nematodes and their hosts, and that TEs are actively mobilizing themselves throughout the life-cycle of two parasitic species. I compare different phylogenetic methods to test for horizontal transfer of TEs between taxa using AviRTE, a LINE element that has been shown previously to have horizontally transferred between birds and parasitic nematodes. I find that phylogenetic trees of TEs based on coding regions differ from trees based on full-length sequences. I identify another TE, RTE1\_Sar, that was horizontally transferred between parasitic nematodes and the common shrew. To rule out contamination of the shrew genome, I develop a pipeline called ConTest that tests for contamination by comparison of TE flanking sequences to two sequence databases. To better understand potential consequences of TE insertions, I investigate underlying mechanism of TE expression. I find that TE expression is specific to developmental stage, and that genes and TEs have potential transcript chimera. This thesis shows that transposons might have transferred more often between parasites and hosts than previously thought, and provides a pipeline to test if a genomic sequence is based on contamination. Furthermore, this work lays an early foundation to study TE impact on parasite genomes by showing that the majority of TE expression arises from read-through transcription, but that younger LINE elements are active and continue to shape genome evolution.
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    Improved Resolution of Prevotella Species, Strains and Genes Reveals TheirDiversity and Virulence Potential in the Female Genital Tract
    (2021-01-29) Bagheri, Sahar; Sycuro, Laura K; Poissant, Jocelyn; Devinney, Rebekah; Lynch, Tarah; Geuking, Markus B
    Bacteria belonging to the genus Prevotella inhabit numerous human body sites, including the female genital tract. Although Prevotella species commonly, and often benignly colonize the vagina, their increased abundance is associated with the dysbiotic condition bacterial vaginosis (BV). Prevotella isolates are also routinely cultured from women experiencing upper genital tract infection and the genus has repeatedly been associated with preterm birth, but the ascending species and mechanisms involved are poorly understood. I developed a new bioinformatics tool that enabled me to ask, for the first time, whether genital Prevotella species encode the Type IX Secretion System, a feature that could contribute to their niche adaptation and virulence (Chapter II). The other objective of my thesis was to better define the phylogenetic breadth and genomic heterogeneity of Prevotella species that colonize the female genital tract. I sought to advance our understanding of how Prevotella impacts human pregnancy by: 1) Identifying the most prevalent and abundant Prevotella species in the lower vs. upper female genital tract; and 2) Performing the first comparative genomics study of the two most common vaginal Prevotella species, P. bivia and P. amnii, which have both been associated with preterm birth. I undertook these analyses using a multidisciplinary approach that included a systematic literature review (Chapter III), pangenome analysis (Chapter III), and a bioinformatics meta-analysis of 19 published microbiome datasets (Chapter IV). My research showed that genital Prevotella populations are much more diverse than previously appreciated, although relatively few genital Prevotella species were consistently detected in high abundance across cohorts. The correlated distribution of Prevotella species prevalence in the lower and upper genital tract suggests they may translocate via broadly conserved or passive mechanisms.The two most prevalent and closely related genital tract Prevotella species are genomically and functionally heterogeneous. Their distinct evolutionary history, driven by horizontal gene transfer and genome reduction, reflects both acquisition and loss of genes involved in evasion, adaptation, and niche partitioning. By expanding our understanding of genital Prevotella species diversity, and establishing parameters for their sensitive and specific detection, this work lays the foundation for future studies that will define the predictive and causal roles these enigmatic bacteria play in reproductive health.
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    A metabolomic- and transcriptomic-level investigation of ant brains infected with the lancet liver fluke Dicrocoelium dendriticum
    (2022-12-22) Li, Chenhua; Wasmuth, James; Goater, Cameron; Cartar, Ralph; Lynch, Tarah
    Parasites often manipulate host phenotypes to facilitate their own transmission. Wood ants, Formica aserva, infected with larvae of the lancet liver fluke, Dicrocoelium dendriticum, leave their nests during the cool hours of the day to ascend and attached to a plant, where they remain overnight, and detach the next morning when temperatures rise returning to their nest. They repeat this bizarre attachment and detachment sequence for the rest of the summer. My thesis seeks to understand the molecular mechanisms that underlie this complex manipulation of host behaviour that is ‘on-then-off’ through metabolomics and transcriptomics approaches. I first characterized changes in the metabolite concentrations in ant brains collected from a site of D. dendriticum emergence in southern Alberta, Canada. Within the laboratory, I recreated the manipulation cycle to mimic pre-attached, attached, and post-attached stages, and sampled infected and uninfected ant brains from each stage. Mean brain concentration of neurotransmitters tyramine and serotonin were reduced in infected ants compared to uninfected during detachment phases by 22% and 17%, respectively. These reductions paralleled a 40% reduction in overall host activity in infected versus uninfected ants during the detachment phase. I then compared the gene expression pattern of brains from infected and uninfected ants at the same samples stages as above. I found that 13,556 genes were differentially expressed, including those involved in environmental sensing and the production of biogenic monoamines. I found genes involved in odorant and vision were downregulated in attached infected ants. Vision genes were upregulated in post-attached infected ants compared to uninfected controls. Genes involved in serotonin synthesis were also downregulated during the post-attached stages in infected ants. These results support that the regulation of biogenic monoamines in the brains of infected ants plays a role in this complex manipulation of host behaviour. Overall, this study helps us better understand how D. dendriticum manipulates their ant host behaviour. My findings show that the mechanisms driving reversible manipulations is more complex than the parasite-induced control of ‘on-then-off’ triggers. In the D. dendriticum-ant system, different mechanisms are involved at different stages of the manipulation.
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    Resolving Complex Microbial Populations and Transmission Networks Through Haplotype Reconstruction
    (2019-07-10) Mak, Lauren; Long, Quan; Lynch, Tarah; De Koning, A. P. Jason
    Next-generation sequencing (NGS) is frequently applied to a mixture of genomes from a complex population that has to be bulk-sequenced. For instance, in virology, the outcome of viral sequencing is generally a mixture of different viruses called ‘quasispecies’. For downstream analyses such as within-host evolution, the quasispecies need to be reconstructed by de-convoluting the aggregated variation data in silico. In this project, I have contributed to the fields of within- and between-host evolutionary analysis by 1) designing and implementing a state-of-the-art haplotype reconstruction program, PoolHapX and 2) quantifying the accuracy of transmission relationship inference from patient pathogen consensus sequences. Existing haplotype reconstruction tools usually use either read-based genomics information or statistics-based linkage sharing across population(s). PoolHapX is the first haplotype reconstruction tool to integrate read-based genomics information and statistics-based linkage-sharing across the population to handle very long sequences, opening new avenues for study into complex within-host populations. I have additionally demonstrated that with consensus sequences alone, a maximum of 67% of person-to-person transmission relationships can be accurately recovered. In the future, within-host haplotypes will be integrated into transmission inference methods to improve inference accuracy. Improvements in the resolution of within- and between-host linkage patterns will empower local epidemiological control; for example, by identifying the genetic properties of high-risk transmission groups to target for clinical support.