Biology subjects

Gould, A.

Publications and source records attributed to Gould, A..

5 recordsLinked to original sources

bioRxiv2025

Genomic Insights into a Highly Specific Marine Symbiosis Uncovers Geographic Structuring Without Co-Divergence Between Siphamia Cardinalfish and Their Bioluminescent Symbiont

Symbiotic relationships with microorganisms are fundamental to life on Earth, yet relatively little is known about how these interactions persist through time, how they co-evolve, and to which degree they are genetically constrained. In this study, three cardinalfish species in the genus Siphamia, S. tubifer, S. mossambica, and S. fuscolineata, were analyzed for patterns of genetic divergence along with their luminous bacterial symbionts, from locations throughout the hosts broad Indo-Pacific distribution. Using whole genome sequencing (WGS) of the fish light organ, we investigated whether the specificity of the association is maintained across host species and over this geographic range and whether there are any patterns of symbiont divergence associated with either. Our results indicated that the light organ symbionts of all three Siphamia species examined were identified as Photobacterium mandapamensis, suggesting a high degree of specificity of the symbiosis is conserved across hosts and geography. There was evidence of biogeographic structure in the symbiont between the three sampling regions, but no co-diversification between the hosts and their symbionts (p = 0.92). However, an analysis of single nucleotide polymorphisms (SNPs) between two S. tubifer populations sampled from Japan and the Philippines indicated some genetic differentiation (FST = 0.043) with phylogenetically-distinct clades of symbionts. Overall, these findings indicate that the association between Siphamia hosts and P. mandapamensis is highly conserved, yet there is significant genetic diversity within the symbionts driven by geography and potentially host ecology.

evolutionary biology↗

bioRxiv2025

A functional comparison of two transplantable syngeneic mouse models of melanoma: B16F0 and YUMM1.7

The B16 murine melanoma cell lines are considered the gold standard for testing melanoma immunotherapies due to low treatment success rates. However, the clinical relevance of these models has been questioned due to a mutational landscape void of driver mutations typically seen in human melanomas and a tendency to form necrotic cores at high tumor volumes. Creating the YUMM1.7 line addressed these limitations by providing an additional contextually consistent model with a more clinically relevant genetic background. The combined use of both models can generate stronger studies in melanoma immunology and immunotherapy. However, to date, there have been no direct functional comparisons of the characteristics of these two models to inform the design of such studies. To address this, we conducted a series of functional experiments to characterize the kinetics of tumor growth, chemotherapeutic sensitivity, and immunogenicity of these models. We found that the B16F0 model had faster intrinsic tumor growth rates, was more susceptible to lysis by tumor-specific CD8+ T cells, and secreted higher levels of the angiogenic factors VEGF and Ang2. Meanwhile, the YUMM1.7 model was more sensitive to chemotherapeutic treatment, secreted higher levels of chemokines CCL2, CXCL1, and CX3CL1, and showed higher infiltration of lymphocyte and myeloid subsets at the same tumor size. Overall, YUMM1.7 model may be better suited for in vivo studies of mechanisms that require a wider observation window and intervention than the B16F0 model, such as immune response. However, angiogenesis and immunotherapy studies may benefit from a more in-depth comparative analyses of both models.

cancer biology↗

bioRxiv2024

MAPK/ERK signaling in gliomas modulates interferon responses, T cell recruitment, enhances tumor-microglia crosstalk, and drives immune checkpoint blockade efficacy.

BackgroundGlioblastoma (GB) remains a formidable challenge in neuro-oncology, with immune checkpoint blockade (ICB) showing limited efficacy in unselected patients. We previously recently established that MAPK/ERK signaling is associated with overall survival following anti-PD-1 and anti-CTLA-4 treatment in recurrent GB. However, the causal relationship between MAPK/ERK signaling and susceptibility to ICB, as well as the mechanisms underlying this association, remain poorly understood. MethodWe conducted in vivo kinome-wide CRISPR/Cas9 screenings in murine gliomas to identify key regulators of susceptibility to anti-PD-1 and CD8+ T cell responses and performed survival studies to validate the most relevant genes. Additionally, paired single cell RNA- sequencing (scRNA-seq) with p-ERK staining, spatial transcriptomics on GB samples, and ex-vivo slice culture of a BRAFV600E mutant GB tumor treated with BRAFi/MEKi were used to determine the causal relationship between MAPK signaling, tumor cell immunogenicity, and modulation of microglia phenotype. ResultsCRISPR/Cas9 screens identified the MAPK pathway, particularly the RAF-MEK-ERK pathway, as the most critical modulator of glioma susceptibility to CD8+ T cells, and anti-PD-1 across all kinases. Experimentally-induced ERK phosphorylation in gliomas enhanced survival with ICB treatment, led to durable anti-tumoral immunity upon re-challenge and memory T cell infiltration in long-term survivors. Elevated p-ERK in glioma cells correlated with increased interferon responses, antigen presentation and T cell infiltration in GB. Moreover, spatial transcriptomics and scRNA-seq analysis revealed the modulation of interferon responses by the MAPK/ERK pathway in BRAFV600E human GB cells with ERK1/2 knockout and in slice cultures of human BRAFV600E GB tissue. Notably, BRAFi/MEKi treatment disrupted the interaction between tumor cells and tumor-associated macrophages/microglia in slice cultures from BRAFV600E mutant GB. ConclusionOur data indicate that the MAPK/ERK pathway is a critical regulator of GB cell susceptibility to anti-tumoral immunity, modulating interferon responses, and antigen-presentation in glioma cells, as well as tumor cell interaction with microglia. These findings not only elucidate the mechanistic underpinnings of immunotherapy resistance in GB but also highlight the MAPK/ERK pathway as a promising target for enhancing immunotherapeutic efficacy in this challenging malignancy.

cancer biology↗

bioRxiv2022

Highly contiguous genome assemblies of Photobacterium strains isolatedfrom fish light organs using nanopore sequencing technology

Several species of luminous bacteria in the genus Photobacterium are the light organ symbionts of teleost fishes. Photobacterium leiognathi and its subspecies, P. mandapamensis, in particular, commonly form bioluminescent symbioses with fish hosts in the Leiognathidae and Acropomatidae families as well as with cardinalfish in the genus Siphamia (Apogonidae). These two closely related lineages of Photobacterium are right at the cutoff average nucleotide identity used to delimit bacterial species (95-96%) and show overlapping ecological niches, including their host fish range. However, there are only a few whole genome assemblies available for these bacterial species, particularly for symbiotic strains isolated from fish light organs, that can be used to explore genome evolution of these two lineages. Here we used Oxford Nanopore Technologies sequencing to produce long reads for assembling highly contiguous genomes of Photobacterium strains isolated from fish light organs, including several P. kishitanii strains isolated from deep water fishes. We were able to assemble 31 high-quality genomes with near complete BUSCO scores, many at the chromosome-level, and compare their gene contents, including plasmid genes. In doing so, we discovered a new candidate species of Photobacterium, Candidatus Photobacterium acropomis, which originated from the light organ of the acropomid fish, Acropoma japonicum. We also describe a lack of congruency between the presence of the luxF gene, which is involved in light production, and the phylogenetic relationships between closely related P. leiognathi and P. mandapamensis strains. In contrast, there was strong congruency between luxF and the host fish family of origin, suggesting this gene might be essential to initiate bioluminescent symbioses with certain hosts, including Siphamia and Acropoma species. Our study shows the benefit of using long reads in the assembly of bacterial genomes and outlines an assembly pipeline that results in highly contiguous genomes, even from low-coverage ONT reads.

microbiology↗

bioRxiv2020

Museum genomics illuminate the high specificity of a bioluminescent symbiosis across a genus of reef fish

Symbiotic relationships between bioluminescent bacteria and fishes have evolved multiple times across hundreds of fish taxa, but relatively little is known about the specificity of these associations and how conserved they have been through time. This study describes the degree of specificity of a bioluminescent symbiosis between cardinalfishes in the genus Siphamia and luminous bacteria in the Vibrio family. Primarily using museum specimens, we investigate the co-divergence of host and symbiont and test for patterns of divergence that correlate with both biogeography and time. Contrary to expectations, we determined that the light organ symbionts of all 14 Siphamia species examined belong to one genetic clade of Photobacterium mandapamensis (Clade II), indicating that the association is highly specific and conserved across the host genus. Thus, we did not find evidence of codivergence among hosts and symbionts. We did observe that symbionts hosted by individuals sampled from colder water regions were more divergent, containing more than three times as many single nucleotide polymorphisms than the rest of the symbionts examined. Overall our findings indicate that the symbiosis between Siphamia fishes and P. mandapamensis Clade II has been highly conserved across a broad geographic range and through time despite the facultative nature of the bacterial symbiont. These results suggest that this bioluminescent symbiosis could have played a key role in the evolution of the host genus and that there are conserved mechanisms regulating its specificity that have yet to be defined.

evolutionary biology↗