Biology subjects

Forsythe, A.

Publications and source records attributed to Forsythe, A..

6 recordsLinked to original sources

bioRxiv2026

Lifestyle impacts the oral microbiome of Classical and Post-classical societies in Italy

ObjectivesThe fall of the Roman Empire (476 CE) profoundly affected the lives of its peoples due to the political, administrative, and territorial changes that occurred. The majority of written records of the time focus on the social elite, leaving larger parts of the population understudied. Here, we employ a bioarchaeological approach to understand how differences in lifestyle may be reflected in the oral microbiome of people from different social classes living before and after the fall. Material and MethodsWe analysed shotgun sequencing data from dental calculus, the preserved oral microbiome, of 67 individuals belonging to different social classes from two Classical cemeteries dated to I-III century CE (Lucus Feroniae and Isola Sacra) and one post-Classical cemetery dated to IV-VIII century CE (Selvicciola), all located in proximity to the city of Rome, Italy. ResultsWe detect significant differences in the oral microbiome taxonomic and functional composition across time periods and social classes, with the rural town of Lucus Feroniae standing out compared to its two counterparts. Reliable identification of dietary items was not possible. DiscussionThe distinct oral microbiome of Lucus Feroniae could reflect differences in general health and subsistence practices. The rural position of this community may have mitigated the cyclical food crises that, instead, affected the contemporary Isola Sacra and the later community of Selvicciola, thereby buffering against the nutritional stress observed in these two locations.

genomics↗

bioRxiv2025

ImmuniT Platform for Improved Neoantigen Prediction in Lung Cancer

11.1 IntroductionLung cancer remains the leading cause of cancer-related deaths, with most patients presenting with advanced, treatment-resistant disease. While immunotherapy has improved outcomes for some, most patients fail to mount an effective immune response due to inadequate tumor recognition. Neoantigen-based therapies offer a promising approach to personalized immunotherapy, but current discovery methods can miss immunogenic targets, particularly those with low or heterogeneous expression. To address this, we developed the ImmuniT platform, which enhances neoantigen identification by amplifying patient-specific targets from primary tumor samples, improving prediction accuracy for more precise immunotherapy. 1.2 MethodsPatients with lung cancer were recruited under an IRB-approved protocol, and freshly resected tumor tissue and matched blood samples were collected. Tumors were processed into single-cell suspensions, enriched for EpCAM+ epithelial cells, and treated to enhance neoantigen expression. Peripheral blood and tumor-infiltrating lymphocytes were co-cultured with cancer cells to expand neoantigen-reactive T cells. The nextneopi pipeline integrated tumor mutational burden (TMB), HLA typing, and transcriptomic data to predict immunogenic targets. MHC:epitope complexes were validated via tetramer staining to identify patient-derived, neoantigen-specific T cells. 1.3 ResultsThe ImmuniT platform demonstrated superior neoantigen prediction and T cell activation in vitro compared to conventional methods across five NSCLC patients. In one patient, it identified two neoantigens missed by standard approaches, which were validated based on their ability to stimulate tumor-infiltrating and peripheral blood lymphocytes. Across all tested samples, the platform identified a broader spectrum of immunogenic targets. These findings highlight its potential to enhance neoantigen discovery and improve personalized immunotherapy strategies. 1.4 ConclusionOur findings indicate that the ImmuniT platform improves neoantigen detection in NSCLC by identifying a wider range of tumor-specific antigens, including those over-looked by conventional methods. By expanding the pool of targetable neoantigens, this technology has the potential to enhance T cell activation and optimize immunotherapy. The ImmuniT platform represents a promising advancement towards more effective, personalized treatment strategies for lung cancer patients, particularly those who do not respond to current immunotherapies.

immunology↗

bioRxiv2025

The role of toxin/antidote genes in the maintenance and evolution of accessory chromosomes in Fusarium

The genomic diversity of many fungal species is augmented by accessory chromosomes, which are variably present in individual strains. These genomic regions evolve rapidly, accumulating genes important in pathogenicity but also harboring significant amounts of transposable elements (TEs). This duality suggests a trade-off: accessory chromosomes provide infection-related benefits while otherwise being deleterious due to their highly repetitive nature and contributions to genomic instability. Despite this, accessory chromosomes often appear to be stably maintained even when strains are grown on media, with no plant host. Previously, we had observed that genes homologous to meiotic drive toxin/antidote proteins from Podospora anserina (Spoks) are abundant on accessory chromosomes in various Fusarium species. Using a functionality screen in yeast, we demonstrate that some of these homologs have active toxin and antidote properties. We propose that these selfish genes act to maintain accessory chromosomes during vegetative growth and may influence their spread via parasexual cycles. Finally, as Spok genes are mobilized by the newly described TE superfamily Starships, it suggests these TEs play crucial roles in forming accessory chromosomes and regions. These results illuminate a mysterious facet of fungal biology, a key step towards describing the origin, spread, and maintenance of pathogenicity in many fungal species.

evolutionary biology↗

bioRxiv2024

Giant transposons promote strain heterogeneity in a major fungal pathogen

Fungal infections are difficult to prevent and treat in large part due to strain heterogeneity which confounds diagnostic predictability. Yet the genetic mechanisms driving strain-to-strain variation remain poorly understood. Here, we determined the extent to which Starships--giant transposons capable of mobilizing numerous fungal genes--generate genetic and phenotypic variability in the opportunistic human pathogen Aspergillus fumigatus. We analyzed 519 diverse strains, including 11 newly sequenced with long-read technology and multiple isolates of the same reference strain, to reveal 20 distinct Starships that are generating genomic heterogeneity over timescales relevant for experimental reproducibility. Starship-mobilized genes encode diverse functions, including known biofilm-related virulence factors and biosynthetic gene clusters, and many are differentially expressed during infection and antifungal exposure in a strain-specific manner. These findings support a new model of fungal evolution wherein Starships help generate variation in genome structure, gene content and expression among fungal strains. Together, our results demonstrate that Starships are a previously hidden mechanism generating genotypic and, in turn, phenotypic heterogeneity in a major human fungal pathogen. ImportanceNo "one size fits all" option exists for treating fungal infections in large part due to genetic and phenotypic variability among strains. Accounting for strain heterogeneity is thus fundamental for developing efficacious treatments and strategies for safeguarding human health. Here, we report significant progress towards achieving this goal by uncovering a previously hidden mechanism generating heterogeneity in the human fungal pathogen Aspergillus fumigatus: giant transposons called Starships that span dozens of kilobases and mobilize fungal genes as cargo. By conducting a systematic investigation of these unusual transposons in a single fungal species, we demonstrate their contributions to population-level variation at the genome, pangenome and transcriptome levels. The Starship compendium we develop will not only help predict variation introduced by these elements in laboratory experiments but will serve as a foundational resource for determining how Starships impact clinically-relevant phenotypes, such as antifungal resistance and pathogenicity.

microbiology↗

bioRxiv2022

Dental calculus metagenomics suggest that ecology, not host phylogeny, shapes the oral microbiome in closely related species

Host-associated microbiomes are essential for a multitude of biological processes. Placed at the contact zone between external and internal environments, the little-studied oral microbiome has important roles in host physiology and health. Here we investigate the contribution of host evolutionary relationships and ecology in shaping the oral microbiome in three closely related gorilla subspecies (mountain, Grauers, and western lowland gorillas) using shotgun metagenomics of 46 museum-preserved dental calculus samples. We find that the oral microbiomes of mountain gorillas are functionally and taxonomically distinct from the other two subspecies, despite close evolutionary relationships and geographic proximity with Grauers gorillas. Grauers gorillas show intermediate bacterial taxonomic and functional, and dietary profiles. Altitudinal differences in gorilla subspecies ranges appear to explain these patterns, proposing a close connection between dental calculus microbiome and the environment, which is further supported by the presence of gorilla subspecies-specific phyllosphere/rhizosphere taxa. Mountain gorillas show high abundance of nitrate-reducing oral taxa, which may contribute to high altitude adaptation by modulating blood pressure. Our results suggest that ecology, rather than evolutionary relationships and geographic proximity, primarily shape the oral microbiome in these closely related species.

evolutionary biology↗

bioRxiv2020

Dimerization of a membrane transporter is driven by differential energetics of lipid solvation of dissociated and associated states

Over two-thirds of integral membrane proteins of known structure assemble into oligomers. Yet, the forces that drive the association of these proteins remain to be delineated, as the lipid bilayer is a solvent environment that is both structurally and chemically complex. In this study we reveal how the lipid solvent defines the dimerization equilibrium of the CLC-ec1 Cl-/H+ antiporter. Integrating experimental and computational approaches, we show that monomers associate to avoid a thinned-membrane defect caused by their exposed dimerization interfaces. In this defect, lipids are strongly tilted and less densely packed than in the bulk, with a larger degree of entanglement between opposing leaflets and greater water penetration into the bilayer interior. Dimerization restores the membrane to a near-native state and therefore, appears to be driven by the larger free-energy cost of lipid solvation of the dissociated protomers. Supporting this theory, we demonstrate that addition of short-chain lipids strongly shifts the dimerization equilibrium towards the monomeric state, and show that the cause of this effect is that these lipids preferentially solvate the defect. Importantly, we show that this shift requires only minimal quantities of short-chain lipids, with no measurable impact on either the macroscopic physical state of the membrane or the proteins biological function. Based on these observations, we posit that free-energy differentials for local lipid solvation define membrane-protein association equilibria. With this, we argue that preferential lipid solvation is a plausible cellular mechanism for lipid regulation of oligomerization processes, as it can occur at low concentrations and does not require global changes in membrane properties. IMPACT STATEMENTDifferences in the lipid solvation energetics of associated and dissociated states is a primary driving force for membrane protein oligomerization, presenting a molecular mechanism for lipid regulation in biology.

biophysics↗