Guyot, M. | Search bioRxiv

bioRxiv2025

A scalable architecture for tuning multistate differentiation ratios in synthetic microbial consortia

Establishing synthetic microbial consortia in competitive environments is often compromised by stochastic colonization bottlenecks, where founder effects lead to the unpredictable dominance of a single strain. Here, we overcome this challenge by engineering a differentiation abacus, a scalable, single-layer recombinase architecture that enables a single progenitor cell to differentiate into up to twelve distinct subpopulations. By arranging competitive excision sites in a linear array, we demonstrate that differentiation ratios can be programmed through rationally tuning recombination-site kinetics and inter-site spacing. This architecture allows the generation of strictly mutually exclusive phenotypes with tunable composition, scaling from simple two-state systems to complex multi-state ensembles without the need for multilayered regulation. Finally, we validate the systems utility in a mouse tumor model, showing that in situ differentiation establishes robust, homogeneous consortia that overcome the colonization variability associated with pre-assembled mixtures. This work provides a versatile and scalable framework for reliably controlling consortia composition for bioproduction, synthetic ecology, and engineered living therapies.

synthetic biology↗

bioRxiv2025

Distinct tumor immune microenvironmental (TIME) landscapes drive divergent immunotherapy responses in glioblastoma

BackgroundImmunotherapies have improved outcomes in many cancers but show limited efficacy in glioblastoma (GBM). This study aimed to determine whether immunotherapy could be tailored to GBM by functional subtyping of vascular-immune landscapes. MethodsWe employed single-cell RNA sequencing, multiplex immunohistochemistry to characterize three distinct TIME subtypes in human and murine GBMs. We evaluated responses to combination of anti-angiogenic immunomodulating therapies (CD40 Ag, anti-PDL1, PI3K{gamma}/{delta} inhibition) in orthotopic syngeneic GBM mouse models. ResultsWe identified three distinct functional TIME subtypes with unique vascular-immune landscapes in human and murine GBM: TIME-low (immune-low/deserted, leaky vasculature), TIME-med (intermediate immune-infiltration, angiogenic), and TIME-high (heavily infiltrated with immunosuppressive myeloid cells and dysfunctional T cells). Representative mouse models of TIME-GBMs responded in subtype specific ways to anti-angiogenic immunomodulating therapies. TIME-low GBMs enhanced T-cell activity but relapsed due to emerging myeloid immunosuppression, concomitant with mesenchymal transition. TIME-med displayed the most immune-activated, yet angiogenic phenotype, and showed overall good responses to various anti-angiogenic immunomodulating therapies. TIME-high GBMs were mostly non-responsive but improved when the myeloid-cell PI3K{gamma} was targeted. However, CD40 agonist treatment, expected to enhance APC function, unexpectedly worsened survival by promoting angiogenesis and heightening immunosuppression, leading to dysfunctional T cells and reduced NK cell recruitment, and subsequent enhanced tumor propagation. ConclusionsOur study reveals three GBM TIME subtypes with distinct vascular-immune landscapes that require tailored therapies. TIME-med tumors are predicted to respond best to immunotherapies, TIME-low tumors show transient effects with anti-angiogenic immunomodulating therapies, while TIME-high tumors, due to their profound immunosuppression, can even have worse outcomes. Key pointsO_LIThree TIME subtypes were identified in GBM with distinct vascular-immune landscapes C_LIO_LITIME subtypes show divergent immunotherapy responses C_LIO_LITIME classification supports personalized treatment strategy for GBM immunotherapy C_LI Importance of the StudyThis study advances glioblastoma immunotherapy by providing the first comprehensive single-cell characterization of TIME subtypes, moving beyond bulk RNA-sequencing to reveal detailed functional states of immune cells. We establish clinically relevant murine models that recapitulate human TIME subtypes, enabling preclinical testing of TIME-targeted therapies. Our findings identify TIME-low GBM as immune deserted and TIME-med tumors as the most immunotherapy-responsive subtype that should be prioritized for clinical selection. We found that high immune infiltration correlates with non-responsiveness and even unexpected detrimental effects with CD40 agonist treatment in TIME-high tumors--critical information given ongoing clinical trials. Identifying distinct immunosuppressive mechanisms across TIME subtypes and differential treatment responses provides a framework for personalized immunotherapy selection. The immediate translational impact of this work highlights the importance of TIME classification for treatment stratification and the urgent need to consider TIME status in clinical trial design, potentially explaining variable patient responses in previous GBM immunotherapy trials.

cancer biology↗

bioRxiv2025

Autophagy maintains HEV identity and function during inflammation

High endothelial venules (HEVs) play a crucial role in adaptive immune responses in secondary and tertiary lymphoid organs. They are uniquely equipped with high levels of peripheral node addressins (PNAd), harboring carbohydrate structures that serve as L-Selectin ligands to efficiently facilitate lymphocyte homing. During inflammation, the HEV network expands in SLOs, increasing lymphocyte infiltration, but the underlying mechanisms maintaining HEVs remain underexplored. Here, we report that autophagy is essential for HEV function and expansion. Using single-cell transcriptomics, intravital imaging, and an inducible HEV tracer system in mice, we demonstrate that autophagy deficiency compromises LT{beta}R-signaling and the Unfolded Protein Response in HEVs, leading to disrupted PNAd production, dedifferentiation, and reduced lymphocyte homing. Autophagy deficiency and LT{beta}R blockade impaired HEV function and reduced skin inflammation in psoriasis-bearing mice by limiting immune infiltration and cytokine release. Our work uncovers an unprecedented role of autophagy in safeguarding HEV identity and function during inflammation. HighlightsO_LIHigh endothelial venules (HEVs) exhibit heightened autophagy in comparison to non-HEV blood endothelial cells, which further increases during inflammation. C_LIO_LIAutophagy is pivotal in maintaining HEV fate and function, specifically during inflammation, via LT{beta}R signaling and the Unfolded Protein Response (UPR), ensuring the proper production of peripheral node addressins (PNAd) that serve as L-selectin ligands for the efficient influx of naive lymphocytes. C_LIO_LIBlocking autophagy in HEVs leads to disrupted PNAd production, HEV flattening and dedifferentiation, and reduced lymphocyte homing. C_LIO_LIGenetic and pharmacological perturbation of HEV function in the lymph nodes and skin lesions of psoriasis-bearing mice impaired neutrophil and lymphocyte recruitment, as well as cytokine secretion, thereby alleviating skin inflammation. C_LI

cell biology↗