Biology subjects

Swartz, A.

Publications and source records attributed to Swartz, A..

5 recordsLinked to original sources

bioRxiv2025

Notch receptors involved in the choice between intestinal secretory and enterocytes and differentiation of Bestrophin 4 cells.

During the first half of embryogenesis, the intestinal epithelium is a simple layer of cuboidal cells surrounded by lateral plate splanchnic mesoderm. As embryogenesis proceeds, the epithelium differentiates to include a variety of enterocytes and secretory cells. During the period of epithelial cell differentiation a number of signaling pathways are used to generate the full complement of cell types. Notch signaling is important for the choice between enterocytes and secretory cells. Following the initial choice, both enterocytes and secretory cells continue differentiating into a number of different subtypes of each cell type. In the zebrafish embryo, Notch signaling is utilized at least three times during development of the intestinal epithelium. The first two Notch signaling events are involved in the choice between enterocytes and secretory cells, while the third involves differentiation of a unique cell type that we previously called Notch Receiving Secretory Cells (NRSCs). While we have identified the times when Notch signaling is active, the individual Notch receptors used in each signaling event have not been previously identified. Here we use loss of function mutants in the four Notch receptors (notch 1a, 1b, 2, and 3) to identify which are used in the each of the Notch signaling events. We find redundant use of Notch receptors in the choice between enterocytes and secretory cells with loss of combinations of either notch 2 and notch 3 or notch 2 and notch 1b but not loss of individual receptors resulting in changes to secretory cell numbers. During the Notch signaling event following the choice between secretory and enterocytes, we identify NRSCs as Bestrophin 4 (BEST4+) cells. In contrast to the choice between secretory and enterocyte cells, we find that loss of individual Notch receptors result in differing numbers of BEST4+ cells. Even though loss of individual receptors affect BEST4+ numbers we suggest that combinations of Notch receptors play a role in differentiation of different BEST4+ subtypes. HighlightsO_LIRequirements for the choice between secretory and enterocytes within the intestinal epithelium require Notch2/Notch3 and Notch2/Notch1b combinations. C_LIO_LINotch 2 and Notch1b are required for Bestropin 4 (BEST4+) cell development. C_LIO_LICombinations of Notch2, Notch1b, and Notch3 may play roles in formation of different BEST4+ subtypes. C_LI

developmental biology↗

bioRxiv2025

IL-12 Secreting CAR-T Cells Reprogram the Tumor Microenvironment and Improve Efficacy Against Heterogeneous Models of Glioblastoma

BackgroundGlioblastoma (GBM) remains uniformly lethal due to pronounced intratumoral heterogeneity and a highly immunosuppressive microenvironment that limits the efficacy of targeted therapies. MethodsWe engineered chimeric antigen receptor (CAR) T cells targeting EGFRvIII and armored them with a single-chain interleukin-12 (scIL12) payload. These cells were tested in syngeneic, orthotopic GBM mouse models exhibiting heterogeneous EGFRvIII expression. CAR T cells were delivered intracranially without lymphodepletion. ResultsIntracranial administration of of scIL12-secreting CAR-T cells eradicated tumors without requiring lymphodepletion, achieving 50% long-term survival. Survival benefits depended entirely on endogenous CD8 T cells, as efficacy was abolished in CD8-deficient hosts and unaffected by NK cell depletion. Notably, therapeutic efficacy was abrogated by lymphodepletion, underscoring the necessity of an intact endogenous immune response. Mechanistically, scIL12 enhanced CAR-T cell persistence and reprogrammed tumor-associated microglia, indicating potential epitope spreading through polyclonal endogenous CD8+ T-cell responses, which facilitate the elimination of EGFRvIII-negative tumor cells. ConclusionsThis study demonstrates the pleiotropic benefits of IL-12 armored CAR-T cells with improved targeting of antigen-positive tumor cells and simultaneous remodeling of the microenvironment to engage adaptive immunity against antigen-negative clones. This strategy offers a potential clinically actionable approach to improve outcomes in GBM by circumventing the need for toxic lymphodepletion and addressing tumor heterogeneity.

immunology↗

bioRxiv2025

Informational Complexity as a Neural Marker of Cognitive Reserve

In Alzheimers disease (AD), a mismatch between neurological damage and cognitive functioning often is attributed to individual differences in cognitive reserve. Understanding the neural mechanism of cognitive reserve could help assessing the therapeutic effectiveness of interventions in AD. To address this, here, 38 elderly participants performed a sustained attention task during high-density EEG while awake and during drowsiness. Operationally, the degree to which performance was impaired under drowsiness signalled the extent of cognitive reserve, with less impairment indicating a higher level of cognitive reserve. Investigating performance variations during the active management of neural challenges offers a novel approach to studying cognitive reserve, capturing dynamics that mirror everyday cognitive demand. We related cognitive reserve to various measures, including informational complexity using the Lempel-Ziv (LZSUM) algorithm. We found a significant interaction effect between arousal and performance, where LZSUM values increased in high performers when drowsy but decreased in low performers. This effect was most pronounced in the frontal and central areas. Our findings suggest LZSUM to be indicative of a compensatory mechanism and thus show potential for LZSUM as a neural marker in assessing cognitive reserve. However, we found no consistent relationship between performance and structural brain measures, and proxies of cognitive reserve. Critically, our findings present a counterexample to the prevailing view that informational complexity purely reflects conscious level. Further research, such as a study with the same paradigm in patients with mild cognitive impairment (MCI) and AD, may lead to additional insights of whether we are truly measuring cognitive reserve.

neuroscience↗

bioRxiv2023

Differentiable Search of Evolutionary Trees from Leaves

Inferring the most probable evolutionary tree given leaf nodes is an important problem in computational biology that reveals the evolutionary relationships between species. Due to the exponential growth of possible tree topologies, finding the best tree in polynomial time becomes computationally infeasible. In this work, we propose a novel differentiable approach as an alternative to traditional heuristic-based combinatorial tree search methods in phylogeny. The optimization objective of interest in this work is to find the most parsimonious tree (i.e., to minimize the total number of evolutionary changes in the tree). We empirically evaluate our method using randomly generated trees of up to 128 leaves, with each node represented by a 256-length protein sequence. Our method exhibits promising convergence (< 1% error for trees up to 32 leaves, < 8% error up to 128 leaves, given only leaf node information), illustrating its potential in much broader phylogenetic inference problems and possible integration with end-to-end differentiable models. The code to reproduce the experiments in this paper can be found at https://github.ramith.io/diff-evol-tree-search.

bioinformatics↗

bioRxiv2023

Orthogonal CRISPR screens to identify transcriptional and epigenetic regulators of human CD8 T cell function

The clinical response to adoptive T cell therapies is strongly associated with transcriptional and epigenetic state. Thus, technologies to discover regulators of T cell gene networks and their corresponding phenotypes have great potential to improve the efficacy of T cell therapies. We developed pooled CRISPR screening approaches with compact epigenome editors to systematically profile the effects of activation and repression of 120 transcription factors and epigenetic modifiers on human CD8+ T cell state. These screens nominated known and novel regulators of T cell phenotypes with BATF3 emerging as a high confidence gene in both screens. We found that BATF3 overexpression promoted specific features of memory T cells such as increased IL7R expression and glycolytic capacity, while attenuating gene programs associated with cytotoxicity, regulatory T cell function, and T cell exhaustion. In the context of chronic antigen stimulation, BATF3 overexpression countered phenotypic and epigenetic signatures of T cell exhaustion. CAR T cells overexpressing BATF3 significantly outperformed control CAR T cells in both in vitro and in vivo tumor models. Moreover, we found that BATF3 programmed a transcriptional profile that correlated with positive clinical response to adoptive T cell therapy. Finally, we performed CRISPR knockout screens with and without BATF3 overexpression to define co-factors and downstream factors of BATF3, as well as other therapeutic targets. These screens pointed to a model where BATF3 interacts with JUNB and IRF4 to regulate gene expression and illuminated several other novel targets for further investigation.

genomics↗