Biology subjects

Bosch, D. E.

Publications and source records attributed to Bosch, D. E..

5 recordsLinked to original sources

bioRxiv2025

Candida albicans infiltrates colon and rectal cancers causing therapeutic resistance and decreased survival

The microbiome is increasingly recognized as a modifier of cancer progression and therapy response, yet the role of intratumoral fungi remains poorly defined. Here, we identify Candida albicans colonization within human colorectal tumors as a predictor of reduced survival and impaired radiation response. Leveraging the Oncology Research Information Exchange Network (ORIEN) cohort, we show that high intratumoral Candida burden is associated with decreased survival across multiple gastrointestinal cancers, with the strongest treatment-specific effect in rectal cancer patients receiving radiotherapy. This observation was validated in independent rectal cancer cohorts using RNA sequencing and quantitative PCR. In immune-competent murine colorectal cancer models, oral gavage of C. albicans resulted in intratumoral colonization, accelerated tumor growth, and radiation resistance, effects not observed with Saccharomyces cerevisiae or PBS controls. Colonized tumors exhibited increased hypoxia, altered metabolic and transcriptional programs, and distinct expression of genes linked to cytokine signaling and cell survival. Hypoxia conditioned C. albicans secreted metabolites that directly conferred radiation resistance to colorectal cancer cells in vitro, implicating a cancer cell intrinsic mechanism independent of immune signaling. Untargeted metabolomics revealed enrichment of nucleosides and lipid oxidation intermediates under hypoxia, suggesting that C. albicans metabolites may provide substrates facilitating tumor recovery after irradiation. These findings establish C. albicans as a causal modifier of tumor biology and radiation response, highlighting intratumoral fungi as future potential therapeutic targets. Modulating fungal colonization or metabolism may improve radiotherapy outcomes and broaden our understanding of interactions between microbes and tumors.

cancer biology↗

bioRxiv2025

Metagenomic polymorphic toxin effector and immunity profiling predicts microbiome development and disease-related dysbiosis

Bacteria use antagonistic interbacterial weapons such as polymorphic toxin secretion systems (TSS) to compete for niches in the human gut microbiome. We developed a bioinformatic marker gene approach (PolyProf) to quantify TSS including [~]200 effector and immunity genes and applied it to [~]15,000 publicly available human metagenomes. PolyProf alpha and beta diversity readily distinguished 12 different human disease states. Decision tree machine learning models integrating bacterial taxonomy with PolyProf had near-perfect accuracy (ROC area 1.00) for all 12 disease states. During microbiome development in the first year of life, PolyProf alpha diversity increases, and beta diversity becomes increasingly like the maternal microbiome, influenced by vertical transfer, delivery mode, and breastfeeding. PolyProf is related to strain sharing among adults through social interactions. In summary, interbacterial antagonism with TSS shapes microbiome development and interpersonal strain sharing. Since PolyProf distinguishes diverse adult disease statuses, these dynamics may contribute to non-genetic inheritance.

microbiology↗

bioRxiv2025

Developing inhibitors of the guanosine triphosphate hydrolysis accelerating activity of Regulator of G protein Signaling-14

Regulator of G protein Signaling-14 (RGS14), an intracellular inactivator of G protein-coupled receptor (GPCR) signaling, is considered an undruggable protein given its shallow and relatively featureless protein-protein interaction interface combined with a distal allosteric site prone to nonspecific inhibition by thiol-reactive compounds. Here, we identify and validate a tractable chemotype that selectively and non-covalently inhibits RGS14 GTPase-accelerating protein (GAP) activity. Combining structure-guided virtual screening, ligand docking across multiple receptor conformers, and enrichment validation, we progressed from a first-generation active, Z90276197, to over 40 second-generation analogs with improved potency. These inhibitors are predicted to engage the solvent-exposed "canyon" in the RGS14 RGS-box that interacts with the G switch I region. Binding pose predictions underscored the importance of non-polar interactions and shape complementarity over polar interactions in engaging this G-binding canyon and revealed an "ambidextrous" pattern of R1- and R2-group orientations. GAP inhibition was confirmed in fluorescence-based and gold-standard radioactive GTP hydrolysis assays. Two second-generation analogs, Z55660043 and Z55627844, inhibited RGS14 GAP activity in both assays and without measurable cytotoxicity. Deep learning-based scoring of predicted docking poses further supported observed affinity gains from R3-group additions. One analog demonstrated favorable in vivo pharmacokinetics and CNS penetration. Collectively, our findings establish tractable, non-covalent, small molecule inhibition of a G protein regulatory interface and illustrate how machine learning-enhanced docking can guide ligand optimization for shallow protein surfaces. This work opens the door to future development of RGS14 inhibitors as potential therapeutics for central nervous system and metabolic disorders.

pharmacology and toxicology↗

bioRxiv2025

Primary tumor microbiomes predict distant metastasis of colorectal cancer

Metastasis causes most cancer-related deaths in colorectal carcinoma (CRC), and microbiome markers may have prognostic value. We hypothesized that primary tumor microbiomes predict distant metastases. We analyzed 5-year metastasis-free survival (MFS) in a retrospective cohort of 900 ORIEN CRC tumor microbiomes (RNAseq). ORIEN findings were validated on an independent cohort using 16S rDNA sequencing and pathobiont-specific qPCR. Microbiome alpha diversity was higher in primary tumors than metastases and positively correlated with metastasis risk. Microbiome beta diversity distinguished primary vs. metastasis and predicted 5-year MFS. High primary tumor abundance of B. fragilis and low F. nucleatum were associated with short MFS. Enterobacteriaceae, including E. coli, were enriched in metastases. qPCR identified increased enterotoxigenic B. fragilis and pks+ E. coli detection in CRC metastasizers. Microbial co-occurrence analysis identified a 3-species clique that predicts metastasis (OR 1.9 [1.4-2.6]). Results suggest that primary tumor microbiomes and specific pathobionts are precision markers for metastasis risk.

cancer biology↗

bioRxiv2020

An interbacterial DNA deaminase toxin directly mutagenizes surviving target populations

When bacterial cells come in contact, antagonism mediated by the delivery of toxins frequently ensues. The potential for such encounters to have long-term beneficial consequences in recipient cells has not been investigated. Here we examined the effects of intoxication by DddA, a cytosine deaminase delivered via the type VI secretion system (T6SS) of Burkholderia cenocepacia. Despite its killing potential, we observed that several bacterial species resist DddA and instead accumulate mutations installed by the toxin, indicating that even in the absence of killing, interbacterial toxins can have profound consequences on target populations. Investigation of additional toxins from the deaminase superfamily revealed that mutagenic activity is a common feature of these proteins, including a representative we show targets single-stranded DNA and displays a markedly divergent structure. Our findings suggest that a surprising consequence of antagonistic interactions between bacteria could be the promotion of adaptation via the action of directly mutagenic toxins.

microbiology↗