Biology subjects

Nikolaev, M.

Publications and source records attributed to Nikolaev, M..

3 recordsLinked to original sources

bioRxiv2023

Human intestinal organoids with an autologoustissue-resident immune compartment

The intimate relationship between the epithelium and the immune system is crucial for maintaining tissue homeostasis, with perturbations in epithelial-immune interactions linked to autoimmune disease and cancer. Whereas stem cell-derived organoids are powerful models of tissue-specific epithelial function, these structures lack tissue-resident immune cells that are essential for capturing organ-level processes. We describe human intestinal immuno-organoids (IIOs), formed through self-organization of epithelial organoids and autologous tissue-resident lymphocytes (TRMs), a portion of which integrate within the IIO epithelium and survey the barrier. IIO formation was driven by TRM migration and interaction with epithelial cells, as orchestrated by TRM-enriched transcriptomic programs governing cell motility and epithelial inspection. We combined IIOs and single-cell transcriptomics to investigate intestinal inflammation triggered by cancer-targeting biologics in patients, and found that the system recapitulates clinical outcomes and the underlying cellular mechanisms. Inflammation was associated with the emergence of an activated population of CD8+ T cells, which progressively acquired intraepithelial and cytotoxic features. The appearance of this effector population was preceded and likely mediated by a Th1-like CD4+ population, which initially displayed a cytokine-producing character and subsequently became cytotoxic itself. A system amenable to direct perturbation and interrogation, IIOs allowed us to identify the Rho pathway as a novel target for mitigating immunotherapy-associated intestinal inflammation. Given that they recapitulate both the phenotypic outcomes and the underlying inter-lineage immune interactions, IIOs can be used to broadly study tissue-resident immune responses in the context of tumorigenesis, infectious and autoimmune diseases.

immunology↗

bioRxiv2023

Bioengineered human colon organoids with in vivo-like complexity and function

Organoids and microphysiological systems, such as organs-on-a-chip, have emerged as powerful tools for modeling human gut physiology and disease in vitro. However, although physiologically relevant, these systems often lack the environmental milieu, spatial organization, cell-type diversity, and maturity necessary for mimicking adult human intestinal mucosa. To instead generate models closely resembling the in vivo cell-type composition and spatial compartmentalization, we herein integrated organoid and organ-on-a-chip technology to develop a primary human stem-cell-derived organoid model, called mini-colons. The luminal access and flow in human mini-colons removes shed cells to greatly enhance tissue longevity and differentiation over physically inaccessible human intestinal organoids that accumulate trapped cellular debris and waste. By establishing a gradient of growth factors, we replicated and sustained in vivo-like cell fate patterning and concurrent differentiation to secretory cell types and colonocytes. These long-lived human mini-colons contain abundant mucus-producing Goblet cells that lubricate the colonic epithelial lining. The stem and proliferative progenitor cells are also realistically confined to the crypts, facilitating stable homeostatic tissue turnover and preserving tissue integrity for several weeks. Also signifying mini-colon in vivo-like maturation, single-cell RNA sequencing showed emerging mature colonocytes and absorptive BEST4+ colonocytes. This methodology could be expanded to generate microtissues derived from the small intestine and incorporate additional microenvironmental components, thus emulating the intricate complexity of the native gut in an in vitro setting. Our bioengineered human organoids provide a highly accurate, long-lived, functional platform to systematically study human gut physiology and pathology, and for the development of novel therapeutic strategies.

bioengineering↗

bioRxiv2022

COORDINATION BETWEEN EMBRYO GROWTH AND TROPHOBLAST MIGRATION UPON IMPLANTATION DELINEATES MOUSE EMBRYOGENESIS

Implantation marks a key transition in mammalian development. The role of embryo-uterus interaction in periimplantation development is however poorly understood due to inaccessibility in utero. Here, we develop an engineered uterus-like microenvironment to recapitulate mouse development ex vivo up to E5.25 and discover an essential role of integrin-mediated trophoblast adhesion to the uterine matrix. Light-sheet microscopy shows that trophoblast cells undergo Rac1-dependent collective migration upon implantation, displacing Reicherts membrane and generating space for egg cylinder growth. The key role of coordination between trophoblast migration and embryo growth is verified by experimentally manipulating the migration velocity and geometry of the engineered uterus. Modeling the implanting embryo as a wetting droplet links the tissue shape dynamics to underlying changes in trophoblast adhesion and suggests that the corresponding tension release facilitates egg cylinder formation. Together, this study provides mechanisms by which dynamic embryo-uterus interactions play an essential role in peri-implantation development.

developmental biology↗