bioRxiv Science⌕ Search
Home/Archive/bioRxiv

bioRxiv · 10.1101/2020.11.29.402735

Microfluidic Device Facilitates Novel In Vitro Modeling of Human Neonatal Necrotizing Enterocolitis-on-a-Chip

Lanik, W. E.·Luke, C. J.·Nolan, L. S.·Gong, Q.·Rimer, J. M.·Gale, S. E.·Luc, R.·Bidani, S. S.·Sibald, C. A.·Lewis, A. N.·Mihi, B.·Agrawal, P.·Goree, M.·Maestas, M.·Hu, E.·Peters, D. G.·Good, M.
View original source ↗Export metadata ↓

Abstract

Necrotizing enterocolitis (NEC) is a deadly gastrointestinal disease of premature infants characterized by an exaggerated inflammatory response, dysbiosis of the gut microbiome, decreased epithelial cell proliferation, and gut barrier disruption. Here, we describe a novel in vitro model of human neonatal small intestinal epithelium (Neonatal-Intestine-on-a-Chip) that mimics key features of intestinal physiology by utilizing a combination of premature infant intestinal enteroids co-cultured with human intestinal microvascular endothelial cells within a microfluidic device. We used our Neonatal-Intestine-on-a-Chip to recapitulate NEC pathophysiology in an in vitro model system of the premature gut inoculated with infant-derived microbiota. This model, also known as NEC-on-a-Chip, emulates the prominent features of NEC, demonstrating significant upregulation of pro-inflammatory cytokines, decreased intestinal epithelial cell markers, reduced epithelial proliferation and disrupted epithelial barrier integrity. NEC-on-a-Chip provides a novel preclinical model of NEC, which may be used as a personalized medicine approach to test new therapeutics for this devastating disease.

Source connections

Explore related subjects

cell biologyPreprint

Keep this discovery

Explore connections, maps & timelines

BibTeXRIS

Lanik, W. E., Luke, C. J., Nolan, L. S., Gong, Q., Rimer, J. M., Gale, S. E., Luc, R., Bidani, S. S., Sibald, C. A., Lewis, A. N., Mihi, B., Agrawal, P., Goree, M., Maestas, M., Hu, E., Peters, D. G., Good, M.. 2020-11-29. Microfluidic Device Facilitates Novel In Vitro Modeling of Human Neonatal Necrotizing Enterocolitis-on-a-Chip. https://doi.org/10.1101/2020.11.29.402735

Cite the original work for its findings. Save a collection to share your selection of sources.

KEEP EXPLORING

Related preprints

bioRxiv2026

High-content screening identifies FDA-approved activators of mitophagy

Mitochondrial diseases are highly heterogeneous disorders caused by defects in oxidative phosphorylation, for which only limited therapeutic options are available. The elimination of dysfunctional mitochondria via mitophagy activation is an attractive strategy to treat several mitochondrial diseases, irrespective of the underlying genetic defect. To identify pharmacological activators of this pathway, we performed a high-content screening of 1,971 FDA-approved compounds using cellular reporters of TFEB nuclear translocation and mitophagy. This screening identified 294 compounds that promoted TFEB translocation, nine of which increased the number of mitolysosomes without compromising cell viability or damaging mitochondria. Among the selected compounds, Meptazinol and Ponatinib emerged as the top-ranked mitophagy inducers in fibroblasts from patients with complex I and IV deficiency, respectively, and were prioritised for further characterisation. However, they did not rescue the bioenergetic defect, suggesting that the stimulation of mitophagy per se is not sufficient to ameliorate the OXPHOS defect in mitochondrial diseases. Overall, our findings establish a scalable platform for the identification of pharmacological activators of TFEB and identify candidate compounds for therapeutic modulation of mitophagy.

cell biology↗
bioRxiv2026

A LOV-domain photoreceptor mediates phototaxis in brown algae

Phototaxis enables motile cells to navigate light environments and plays a critical role in survival and reproduction across diverse eukaryotic lineages. This ability has evolved independently through distinct photoreceptor systems. Yet, the molecular mechanisms underlying phototaxis remain poorly understood in many major eukaryotic lineages, including stramenopiles. Here, combining functional genetics, cell biology and evolutionary analyses, we identify Helmchrome (HELM), a LOV-domain protein required for phototaxis in the brown alga Ectocarpus. HELM localizes to the posterior flagellum and is responsible for the characteristic flavin-associated fluorescence of brown algal gametes. Loss of HELM abolishes phototactic accumulation and directional orientation without affecting basal motility or fertilization, demonstrating its specific requirement for light-directed movement. Phylogenetic analyses reveal that HELM-like proteins are distributed across diverse stramenopile lineages and that their domain architecture evolved through repeated duplication of an ancestral RGS-LOV module. Our findings identify HELM as a key component of the light-sensing machinery in brown algae, provide a molecular explanation for the long-standing observation of flagellar flavin fluorescence, and reveal a distinct phototaxis system that expands the known diversity of eukaryotic light-sensing mechanisms.

cell biology↗
bioRxiv2026

RCDome: A Multi-Database Human Gene Atlas of Regulated Cell Death

Introduction: Regulated cell death (RCD) governs tissue homeostasis, development, and disease, and is executed or regulated by specific genes. Yet for the researcher asking which genes execute or regulate a given RCD form, the answer is rarely simple: gene lists for the same form rarely agree across databases, many associations carry no traceable source, and most have never been systematically checked against primary literature. We built RCDome to answer the most basic question a researcher can ask: where did this gene-RCD association come from, and what is the evidence? Methods: RCDome is a multi-database human gene atlas built through a staged architecture integrating multi-source compilation, literature validation and evidence recovery, mechanistic classification, human-governed ontological adjudication, and web deployment. Five complementary evidence channels (PubMed Boolean search, curated databases, AI-assisted screening, manual curation, and Elicit systematic review) were integrated from 20 public databases into a unified matrix. Sixty-two original name strings were canonicalized into 53 RCD-related entities with curator-adjudicated operational definitions and ontological levels. Gene-RCD associations were systematically evaluated through an independent DeepSeek two-call LLM validation, Europe PMC full-text recovery and deep evidence extraction, an independent Consensus literature-search channel, and GPT-4o arbitration of disagreements. Source-grounding controls rejected extracted evidence not found verbatim in the source document, while the governance contract was enforced as executable code. Results: The compendium holds 22,473 association rows spanning 9,265 unique HGNC-validated genes (21,568 unique gene-RCD pairs). Evidence-first adjudication resolved 5,138 pairs (23.8%) as mechanistically involved; across the 4,775 role-resolved pairs, 225 (4.7%) are executors, 4,455 (93.3%) are regulators, and 95 are markers, revealing a small death-executing core embedded in a vast regulatory network. Under a separate seven-class mechanistic criterion applied to all 22,473 rows, only 3,063 (13.6%) were mechanistically confirmed and 286 (1.3%) were database-only with no verifiable paper trail. Conclusion: RCDome makes the RCD evidence landscape measurable and traceable, showing that AI-assisted curation can be verifiable, human-governed, and explicit about uncertainty. It is delivered as a Shiny web application that lets any researcher query the atlas and inspect the evidence behind each association. Availability: RCDome is freely available at https://rcdome.org/ (source code and data at https://github.com/BioCancerInformatics/RCDome).

cell biology↗