Biology subjects

Stahl, D.

Publications and source records attributed to Stahl, D..

4 recordsLinked to original sources

bioRxiv2025

Single recipient cell tracking of tellurium-labeled extracellular vesicle proteomes (TeLEV) identifies EV-driven immunomodulation

Extracellular vesicles (EVs) mediate tumor-immune cell communication by carrying protein cargo that can immediately modulate signaling and antigen presentation. Yet mapping the uptake of primary EV proteomes by human immune cells at single-cell resolution has been constrained by a lack of labeling strategies. We show here that TeLEV, a tellurium-based metabolic mass tagging approach that incorporates L-2-tellurienylalanine (TePhe) into EV proteomes, can produce a biologically rare monoisotopic signal, which is detectable by mass cytometry, imaging mass cytometry, and nanoscale SIMS, without perturbing EV morphology, yield, or proteome composition. We applied TeLEV to label primary malignant B-cell-derived EVs (MBC-EVs) from chronic lymphocytic leukemia (CLL) patients and could follow EV uptake by distinct cell populations of healthy donor peripheral blood mononuclear cells. MBC-EV uptake occurred predominantly in cells of myeloid lineages. In direct control experiments with matched secreted proteins, a machine learning approach identified CD123, CD127, and CD25 as key markers distinguishing primary MBC-EV recipients from matched secreted protein recipient cells. Nanoscale imaging enabled localization of EV-delivered proteins within heterochromatin, whereas Te-labeled secreted proteins accumulated in the cytoplasm of recipient cells. We then generated a pan-immune EV uptake atlas by tracing the uptake of primary and cell-line EVs from nine cell lines and six donors with chronic lymphocytic leukemia into 2,977,094 recipient cells across 43 cell types and subpopulations. We found that the uptake of MBC-EVs by myeloid recipients induced monocyte-derived dendritic-cell polarization characterized by the co-expression of the interleukin-receptor triad (IL-RT: CD123, CD127, CD25) identified above. Time-resolved EV uptake analysis showed a rapid, transient expression of CD123/CD127 followed by CD25, both tightly coupled to MBC-EV uptake by myeloid cells. The intensity of IL-RT expression correlated with that of PD-L1 and BCL-2. Using different STAT degraders to bidirectionally modify the EV-induced STAT5 signal, we observed that MBC-EV uptake and IL-RT, PD-L1, and BCL-2 expression increased with STAT3 degradation and decreased with STAT5 degradation. To investigate the functional consequences of the MBC-EV-induced changes, we showed that MBC-EVs in the presence of IL-2 induced a high-CD25 immune state with low cytotoxic and high B cell proliferation. Taken together, TeLEV represents a novel tool for single-cell tracking of EV proteomes, revealing STAT5-dependent immune remodeling of recipient cells.

cancer biology↗

bioRxiv2024

Modest functional diversity decline and pronounced composition shifts of microbial communities in a uranium-contaminated aquifer

BackgroundMicrobial taxonomic diversity declines with increased environmental stress. Yet, few studies have explored whether phylogenetic and functional diversities track taxonomic diversity along the stress gradient. Here, we investigated bacterial communities within an aquifer in Oak Ridge, Tennessee, USA, which is characterized by a broad spectrum of stressors, including extremely high levels of nitrate, heavy metals like cadmium and chromium, radionuclides such as uranium, and extremely low pH (<3). ResultsBoth taxonomic and phylogenetic -diversities were reduced in the most impacted wells, while the decline in functional -diversity was modest and statistically insignificant, indicating a more robust buffering capacity to environmental stress. Differences in functional gene composition (i.e., functional {beta}-diversity) were pronounced in highly contaminated wells, while convergent functional gene composition was observed in uncontaminated wells. The relative abundances of most carbon degradation genes were decreased in contaminated wells, but genes associated with denitrification, adenylylsulfate reduction, and sulfite reduction were increased. Compared to taxonomic and phylogenetic compositions, environmental variables played a more significant role in shaping functional gene composition, suggesting that niche selection could be more closely related to microbial functionality than taxonomy. ConclusionsOverall, we demonstrated that despite a reduced taxonomic -diversity, microbial communities under stress maintained functionality underpinned by environmental selection.

microbiology↗

bioRxiv2023

The diversity and ecological significance of microbial traits potentially involved in B12 biosynthesis in the global ocean

Cobalamin (B12), an essential nutrient and growth cofactor for many living organisms on the Earth, can be fully synthesized only by selected prokaryotes in nature. Therefore, microbial communities related with B12 biosynthesis could serve as an example subsystem to disentangle the underlying ecological mechanisms balancing the function and taxonomy of complex functional assemblages. By anchoring microbial traits potentially involved in B12 biosynthesis, we depict the biogeographic patterns of B12 biosynthesis genes and their carrying taxa in the global ocean, in light of the limitation to detect de novo B12 synthesizers via metagenomes alone. Both the taxonomic and functional composition of B12 biosynthesis genes were strongly shaped by depth, differentiating epipelagic from mesopelagic zones. The functional genes were relatively stably distributed across different oceans, but their carrying taxa varied considerably, showing clear functional redundancy of microbial systems. Microbial taxa carrying B12 biosynthesis genes in the surface water were influenced by environmental factors such as temperature, oxygen and nitrate. However, the composition of functional genes was weakly associated with these environmental factors. Null model analyses demonstrated that determinism governed the compositional variation of B12 biosynthesis genes, whereas a higher degree of stochasticity was associated with taxonomic variations. Significant associations were observed between chlorophyll a concentration and B12 biosynthesis traits, indicating their importance in global ocean primary production. Conclusively, this study revealed an essential ecological mechanism governing the assembly of microbes in nature: the environment selects function rather than taxonomy; functional redundancy underlies stochastic community assembly. Impact StatementA central question in ecology is how a galaxy of microbial taxa is assembled and distributed across space and through time, executing essential ecosystem functions. By anchoring microbial functional traits potentially involved in B12 biosynthesis and their carrying microbial taxa in the global ocean, this study addresses essential ecological questions from functional and taxonomic angles. Integrating multiple lines of evidence, we show that the ecosystem selects functional traits rather than taxonomic groups, and functional redundancy underlies stochastic taxonomic community assembly. Also, microbial communities potentially involved in B12 biosynthesis are significantly associated with chlorophyll a concentration, demonstrating their importance in global ocean primary production. This study provides valuable mechanistic insights into the complex microbial community assembly in natural ecosystems.

microbiology↗

bioRxiv2019

Working Towards a Blood-Derived Gene Expression Biomarker Specific for Alzheimer’s Disease

BackgroundA significant number of studies have investigated the use of blood-derived gene expression profiling as a biomarker for Alzheimers Disease (AD). However, the typical approach of developing classification models trained on subjects with AD and complimentary cognitive healthy controls may result in markers of general illness rather than being AD-specific. Incorporating additional related neurological and age-related disorders during the classification model development process may lead to the discovery of an AD-specific expression signature.\n\nMethodsTwo XGBoost classification models were developed and optimised. The first used the typical approach, training on 160 AD and 160 cognitively normal controls, while the second was trained in 6318 AD and 6318 mixed controls. Up-sampling was performed in each training set to the minority classes to avoid sampling bias, and both classification models were evaluated in an independent dataset consisting of 127 AD and 687 mixed controls. The mixed control group represents a heterogeneous ageing population consisting of Parkinsons Disease, Multiple Sclerosis, Amyotrophic Lateral Sclerosis, Bipolar Disorder, Schizophrenia, Coronary Artery Disease, Rheumatoid Arthritis, Chronic Obstructive Pulmonary Disease, and cognitively healthy subjects.\n\nResultsThe typical approach resulted in a 74 gene classification model with a validation performance of 58.3% sensitivity, 30.3% specificity, 13.4% PPV and 79.7% NPV. In contrast, the second approach resulted in a 28 gene classification model with an overall improved validation performance of 46.5% sensitivity, 95.6% specificity, 66.3% PPV and 90.6% NPV.\n\nConclusionsThe addition of related neurological and age-related disorders into the AD classification model developmental process identified a more AD-specific expression signature, with improved ability to distinguish AD from other related diseases and cognitively healthy controls. However, this was at the cost of sensitivity. Further improvement is still required to identify a robust blood transcriptomic signature specific to AD.

genetics↗