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Biology subjects

Lukonin, I.

Publications and source records attributed to Lukonin, I..

4 recordsLinked to original sources

Organoid-based colorectal tumor microenvironment model for immuno-oncology research

The development of cancer immunotherapies is hindered by the lack of human-relevant models that accurately translate to patient outcomes. We combine patient-derived colorectal tumor organoids (PDOs) and cancer-associated fibroblasts (CAFs) into floating extracellular matrix drops to form miniature colorectal tumors. These SHaking Organoid CO-cultures (SHOCOs) reproducibly capture key features of the tumor microenvironment (TME), including physiologically relevant ECM, hypoxic regions, and a diversified stromal compartment that captures primary CAF states. Compared with traditional PDO-based co-culture models, SHOCOs maintain immune cells in numbers, states and functional interactions that more closely reflect the physiological tumor microenvironment. The modularity of the system allowed controlled simulation of diverse patient tumor archetypes, and defining how TME components shape therapy response. Immune-rich SHOCOs treated with T-cell bispecific antibodies exhibited robust anti-tumor responses that were stronger and more rapid than their PDO-based counterparts. Stroma-rich tumors, on the other hand, diminished therapy responses by physically hindering both immune cell recruitment and limiting antibody penetration. Thus, SHOCOs enable the construction of modular tumor microenvironments, providing a versatile platform to dissect immune and stromal tumor biology and to catalyze the discovery of novel therapeutic approaches.

cancer biology↗

An integrated platform for high-throughput phenospace learning of 3D multilineage organoid systems

Complex multilineage organoid systems lack quantitative phenotyping methods preserving spatial architecture at high throughput. Current approaches compromise biological complexity, spatial resolution, or robust homogeneous multilineage assembly. We establish an integrated experimental-computational platform for high-throughput spatial phenotyping of multilineage organoids through developing a modular tumoroid culture system incorporating pancreatic ductal adenocarcinoma (PDAC) cells and cancer-associated fibroblasts (CAFs) in 384-well format with multiplexed whole-mount imaging. We developed Phenocoder, a machine learning framework combining conditional variational autoencoders with spatial graph analysis to extract multiscale organoid features. Rigorous validation demonstrates robust performance in PDAC tumoroids. The platform identifies pathway modulators that disrupt the fibrotic microenvironment and discovers stroma-dependent vulnerabilities, undetectable in monocultures. Extending to immuno-competent tumoroids, we assess fibrosis modulators in combination with T cell bispecific antibodies, identifying treatments that enhance immune cell proliferation and infiltration inducing cancer cell death, validated in patient-derived explants. This platform establishes a generalizable framework for multilineage organoid phenotyping.

cancer biology↗

Anthrax intoxication reveals that ER-Golgi membrane contact sites control the formation of plasma membrane lipid nanodomains

To promote infections, pathogens exploit host cell machineries including structural elements of the plasma membrane. Studying these interactions and identifying involved molecular players is an ideal way to gain insights into the fundamental biology of the host cell. Here, using the anthrax toxin, we screened a 1500-gene library of regulatory, cell surface, and membrane trafficking genes for their involvement in the intoxication process. We found that the ER-Golgi-localized proteins TMED2 and TMED10 are required for toxin oligomerization at the cell surface, an essential step for anthrax intoxication that depends on localization to cholesterol-rich lipid nanodomains. Further biochemical, morphological and mechanistic analyses showed that TMED2 and TMED10 are essential components of a multiprotein supercomplex that operates exchange of both cholesterol and ceramides at ER-Golgi membrane contact sites. Overall, this study of anthrax intoxication led to the discovery that lipid compositional remodelling at ER-Golgi interfaces fully controls the formation of functional membrane nanodomains at the cell surface.

cell biology↗

REPRESSION BY HDAC3 AND DAX1 MEDIATES LINEAGE RESTRICTION OF EMBRYONIC STEM CELLS

Mouse embryonic stem cells (mESCs) give rise to embryonic but not extraembryonic endoderm fates. Here, we identify the mechanism of this lineage barrier and report that the histone deacetylase Hdac3 and the corepressor Dax1 cooperatively restrict transdifferentiation of mESCs by silencing an enhancer of the extraembryonic endoderm-specifying transcription factor (TF) Gata6. This restriction is opposed by the pluripotency TFs Nr5a2 and Esrrb, which promote cell type conversion. Perturbation of the barrier extends mESC potency, and allows formation of 3D spheroids that mimic the spatial segregation of embryonic epiblast and extraembryonic endoderm in early embryos. Overall, this study shows that transcriptional repressors stabilize pluripotency by biasing the equilibrium between embryonic and extraembryonic lineages that is hardwired into the mESC TF network.

developmental biology↗