Biology subjects

Barnick, B.

Publications and source records attributed to Barnick, B..

4 recordsLinked to original sources

bioRxiv2026

The Urinary Tract Commensal Peptoniphilus spp. Encodes a Novel 17β-Hydroxysteroid Dehydrogenase

Microbial steroid metabolism represents an underappreciated extension of the vertebrate endocrine system, with growing evidence that host-associated microbes contribute to the diversity and bioavailability of sex steroids within human tissues. Emerging studies have linked microbial androgen metabolism to urinary microbiome composition and to resistance to androgen deprivation therapy (ADT) in prostate cancer. While microbial pathways capable of converting steroid precursors such as cortisol to androgens, via the steroid-17,20-desmolase pathway, such as DesG-mediated interconversion of androstenedione to testosterone have been reported, the diversity of enzymes mediating downstream androgen interconversion remains incompletely defined. Here, we investigate the androgen-forming capabilities of anaerobic bacteria from the male genitourinary microbiome, focusing on NADPH-dependent 17{beta}-hydroxysteroid dehydrogenases (17{beta}-HSDHs) that catalyze interconversion of androstenedione and testosterone. We isolated androgen-forming bacterial strains from human male urine and identified a previously uncharacterized 17{beta}-HSDH encoded by Peptoniphilus obesi, demonstrated that this enzyme catalyzes the NADPH-dependent reduction of androstenedione to testosterone and the reverse oxidation reaction. Sequence similarity searches further identified a homologous 17{beta}-HSDH in Anaerococcus, which was synthesized and functionally validated, revealing conserved activity despite low sequence identity to the previously characterized urinary tract enzyme DesG. The enzymes were found to have broad substrate specificity for C19 and C18 17keto- and 17{beta}-hydroxysteroids. Together, these findings expand the known diversity of microbial 17{beta}-HSDHs and identify previously unrecognized androgen-forming activities within the genitourinary microbiome. ImportanceMicrobial steroid-transforming pathways may provide a mechanism by which commensal anaerobes contribute to androgen availability in the genitourinary tract. By identifying novel 17{beta}-hydroxysteroid dehydrogenases from Peptoniphilus and Anaerococcus, genera repeatedly associated with prostate cancer, this study provides mechanistic insight into how microbial steroid metabolism may influence hormone-driven disease.

microbiology↗

bioRxiv2025

The urinary pathobiont Actinobaculum massiliense generates androgens via the dirAB pathway

While overlooked during the Human Microbiome Project, characterizing the urinary microbiota in health and disease is a new frontier in microbiome science. Recent studies have associated differential abundance of bacterial taxa including Propionimicrobium lymphophilum and Actinobaculum/Actinotignum spp. with prostate cancer. In this study, we collected urine from subjects prior to prostate biopsy and applied a novel Human Sterolbiome Discovery High-throughput (HSDH) assay to identify culturable urinary bacteria with the ability to generate androgens. Application of the HSDH assay to urine samples led to the isolation of eight P. lymphophilum strains positive for cortisol side-chain cleavage (steroid-17,20-desmolase), 17{beta}-HSDH activity, or both. In addition, we isolated three strains of Actinobaculum massiliense that encode DHEA isomerase reductase (dir) genes. The dirA gene encodes a novel 3{beta}/17{beta}-hydroxysteroid dehydrogenase/{Delta}4,5-isomerase and the dirB gene encodes a novel 17{beta}-hydroxysteroid dehydrogenase isoform. Structural prediction and molecular dynamics reveal probable catalytic mechanisms based on the shared catalytic triad but distinct binding pocket geometries of the DirA and DirB that describe their respective reactions. Phylogenetic analysis of DirA and DirB revealed homologs in urinary tract commensals as well as bacteria associated with steroid degradation found in aquatic and terrestrial environments. Taken together, the development of the HSDH assay and the identification of the dir pathway genes is a significant advance in microbial endocrinology, laying the methodological foundation and providing the molecular basis for understanding the role of urinary tract bacteria in host endocrine physiology.

microbiology↗

bioRxiv2025

In silico reconstruction of primary and metastatic tumor architecture using GIS-augmented spatial transcriptomics

The tumor microenvironment (TME) comprises different cell populations that interact, contributing to tumor heterogeneity and therapy response. Spatial transcriptomics offers valuable insights into transcriptional complexity and heterogeneity of the TME. We established Geographic Information System (GIS)-augmented In-Silico Reconstruction of Tumor Architecture (GIS-ROTA), a biologically informed analytic framework that integrates pathway or cell type-based enrichment analysis with local Morans I to uncover functional spatial domains. In our Visium dataset of primary and metastatic estrogen receptor-positive breast tumor samples, GIS-ROTA revealed extensive co-localization of estrogen response with metabolic pathway gene sets and mutual exclusivity with metastasis-related and specific immune-related pathway gene sets. The novelty of our approach lies in considering biological functions prior to identifying any spatial domains, providing direct interpretability and minimizing the subjectivity of interpreting clusters observed from conventional analytic methods. Overall, our GIS-ROTA framework integrates biological knowledge first, yielding spatial patterns with functional relevance and enabling identification of novel targets for development of therapeutic strategies.

cancer biology↗

bioRxiv2025

ACSS2-Mediated Metabolic-Epigenetic Crosstalk Drives Fulvestrant Resistance and Represents a Novel Therapeutic Target

1.Endocrine therapies target hormone-dependent cancer cells, primarily through estrogen receptor alpha (ER), expressed in [~]70% of breast cancers (ER+). Despite treatment advances, 30-40% of ER+ breast cancer patients experience recurrence and metastasis, with 5-year survival rates of only 31.9%. We validated poor outcomes for liver metastasis patients treated with Fulvestrant (Fulv) using the local Carle Foundation Hospital cohort and examined metabolic pathways in liver metastatic patient-derived xenograft (PDX) models, revealing upregulated lipid and acetyl-CoA production. Our previous work demonstrated that combining Fulv with acetyl-CoA synthase inhibitor (ACSI) targeting Acyl-CoA Synthetase Short Chain Family Member 2 (ACSS2), synergistically reduced ER+ metastatic breast cancer (MBC) cell viability in vitro. Using multiple analytical approaches-isotope tracing, CUT&RUN sequencing, immunofluorescence, western blot, and RNA sequencing-we characterized the effects of acetyl-CoA synthesis inhibition on Fulv-induced alterations. Fulv treatment of MBC cells increased ACSS2 expression and acetate utilization. Isotope tracing revealed that Fulv decreased acetate flux to the TCA cycle while promoting fatty acid synthesis. Importantly, ACSS2 was predominantly nuclear and CUT&RUN sequencing showed that Fulv treatment increased ACSS2 chromatin occupancy and ER/ACSS2/H3K27ac overlapping sites near genes associated with tumor progression, which was eliminated by combination of ACSI and Fulv. RNA sequencing revealed reduction of Fulv-induced expression of genes involved in cancer cell metabolism and key signaling pathways in cancer with the Fulv+ACSI combination. In a therapy-resistant xenograft model, combining Fulv and ACSI reduced Fulv-dependent increase in metastatic burden. Our findings indicate ACSS2 contributes to endocrine therapy resistance through nuclear acetyl-CoA provision for epigenetic alterations. Targeting these cancer cell adaptations represents a novel therapeutic approach potentially reducing metastasis-related mortality and improving breast cancer treatment outcomes.

cancer biology↗