Intestinal Organoids Research Articles

Abstract 153: Identification of a gastrointestinal (GI) toxicity gene signature that predicts GI-toxicity induction in small intestinal organoids

Abstract The early identification of GI toxicity caused by novel therapeutics is crucial for drug development pipelines. GI toxicity is one of the most frequent adverse effects amongst chemotherapeutics. Impaired barrier function and epithelial ulceration can lead to symptoms including diarrhoea, dehydration and susceptibility to systemic infection. We have identified a gene signature that can be utilised in an in vitro organoid model to predict relevant GI toxicity. Methods: Both mice and small intestinal organoids derived from human and mouse were exposed to chemotherapeutic agents known to cause GI toxicity. For in vivo assays mice were treated with 50 or 100mg/kg CPT11 for 4 or 8 hours or 100, 200 or 400mg/kg Iressa for 8 or 24 hours before small intestinal (SI) tissue was removed for RNA-Seq analysis. SI tissue was also analysed by histological staining and damage measured to confirm induction of GI-toxicity. Human and mouse organoids were treated with CPT11 and Iressa for 8 hours at a range of concentrations. The organoids were lysed, RNA extracted and an mRNA-Seq library was generated. Samples were sequenced using 2 × 75bp PE reads on a Next-Seq550. Sequences were aligned to the relevant genomes using BWA and normalised using DESeq2. Normalised gene counts were analysed using Partek Genomics Suite and Ingenuity Pathway Analysis (IPA) was used for gene set enrichment (GSEA) and pathway analysis of differentially expressed genes. Results: For all treatments and time points the mechanism of action (MOA) of each agent was evident from the GSEA and pathway analysis. CPT11 induced DNA damage and cell cycle arrest pathways, whereas Iressa demonstrated downregulation of cell cycle and chromosomal replication and mitotic genes. Analysis of toxicity pathways in IPA identified a number of differentially expressed genes that were consistent with increased toxicity. A gene signature was identified and a multivariate scoring system used to demonstrate signature engagement. This signature was activated in all SI tissues treated with CPT11 or Iressa, irrespective of the MOA of both agents. Conclusions: Deployment of this signature on mouse and human organoids treated with chemotherapeutic agents demonstrated activation of the signature, which could be an alternative method for GI toxicity testing. Further analysis of this signature in gene expression studies from GI toxicity inducing agents submitted to the NCBI Gene expression omnibus (GEO) demonstrated that the signature was activated with a variety of agents with different MOA’s such as NSAIDs, gamma-secretase inhibitors, CDK8/19 inhibitors and CAR-T-cells. Citation Format: Gary S. Beale, Aude Marine-Bonavita, Valentina Ubertini, Greg Tudor, Francesca Philips, Catherine Booth. Identification of a gastrointestinal (GI) toxicity gene signature that predicts GI-toxicity induction in small intestinal organoids [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 153.

Potential Effect of Glutamine in the Improvement of Intestinal Stem Cell Proliferation and the Alleviation of Burn-Induced Intestinal Injury via Activating YAP: A Preliminary Study

Burn injury is a common form of traumatic injury that leads to high mortality worldwide. A severe burn injury usually induces gut barrier dysfunction, partially resulting from the impairment in the proliferation and self-renewal of intestinal stem cells (ISCs) post burns. As a main energy substance of small intestinal enterocytes, glutamine (Gln) is important for intestinal cell viability and growth, while its roles in ISCs-induced regeneration after burns are still unclear. To demonstrate the potential effects of Gln in improving ISCs proliferation and alleviating burn-induced intestinal injury, in this study, we verified that Gln significantly alleviated small intestine injury in burned mice model. It showed that Gln could significantly decrease the ferroptosis of crypt cells in the ileum, promote the proliferation of ISCs, and repair the crypt. These effects of Gln were also confirmed in the mouse small intestine organoids model. Further research found that Yes-associated protein (YAP) is suppressed after burn injury, and Gln could improve cell proliferation and accelerate the renewal of the damaged intestinal mucosal barrier after burns by activating YAP. YAP is closely associated with the changes in intestinal stem cell proliferation after burn injury and could be served as a potential target for severe burns.

The synthetic aminoglycoside ELX-02 induces readthrough of G550X-CFTR producing superfunctional protein that can be further enhanced by CFTR modulators.

Ten percent of cystic fibrosis (CF) patients carry a premature termination codon (PTC); no mutation-specific therapies exist for these individuals. ELX-02, a synthetic aminoglycoside, suppresses translation termination at PTCs (i.e., readthrough) by promoting the insertion of an amino acid at the PTC and restoring expression of full-length CFTR protein. The identity of amino acids inserted at PTCs affects the processing and function of the resulting full-length CFTR protein. We examined readthrough of the rare G550X-CFTR nonsense mutation due to its unique properties. We found that forskolin-induced swelling in G550X patient-derived intestinal organoids (PDOs) was significantly higher than in G542X PDOs (both UGA PTCs) with ELX-02 treatment, indicating greater CFTR function from the G550X allele. Using mass spectrometry, we identified tryptophan as the sole amino acid inserted in the G550X position during ELX-02- or G418-mediated readthrough, which differs from the three amino acids (cysteine, arginine, and tryptophan) inserted in the G542X position after treatment with G418. Compared with wild-type CFTR, Fischer rat thyroid (FRT) cells expressing the G550W-CFTR variant protein exhibited significantly increased forskolin-activated Cl- conductance, and G550W-CFTR channels showed increased PKA sensitivity and open probability. After treatment with ELX-02 and CFTR correctors, CFTR function rescued from the G550X allele in FRTs reached 20-40% of the wild-type level. These results suggest that readthrough of G550X produces greater CFTR function because of gain-of-function properties of the CFTR readthrough product that stem from its location in the signature LSGGQ motif found in ATP-binding cassette (ABC) transporters. G550X may be a particularly sensitive target for translational readthrough therapy.NEW & NOTEWORTHY We found that forskolin-induced swelling in G550X-CFTR patient-derived intestinal organoids (PDOs) was significantly higher than in G542X-CFTR PDOs after treatment with ELX-02. Tryptophan (W) was the sole amino acid inserted in the G550X position after readthrough. Resulting G550W-CFTR protein exhibited supernormal CFTR activity, PKA sensitivity, and open probability. These results show that aminoglycoside-induced readthrough of G550X produces greater CFTR function because of the gain-of-function properties of the CFTR readthrough product.

Abstract 1107: Exploring the hypoxia pathway for gastrointestinal radioprotection in human minigut model

Abstract Introduction: When pancreatic cancer cannot be removed by surgery, radiation can be used to approximate a resection. Unfortunately, conventional radiation therapy cannot achieve ablative doses in the pancreas due to potential radiotoxicity to the nearby intestinal tissues. Thus, treatment-related gastrointestinal (GI) toxicity may be the most significant barrier to improving treatment responses for unresectable pancreatic cancer. There are no medications that can selectively protect the intestine from radiation damage, but we previously demonstrated that the genetic or pharmacologic inhibition of the EGLN prolyl hydroxylases protects murine intestines from radiation injury. To translate these findings to patients, we sought to test the EGLN inhibitor, FG-4592, and its mechanism of selective radioprotection in patient-derived intestinal organoids (also known as enteroids or mini-guts). Methods: The patient-derived enteroids (PDEs) were grown from duodenal tissue of non-oncologic patients, embedded in Matrigel, and cultured in media impregnated with essential growth factors. These PDEs have the capacity to recapitulate the full array of intestinal cells that are present in the crypt-villus axis. We first treated PDEs with FG-4592 then irradiation at 24 hours followed by RT-qPCR at 72 hrs post-exposure to gauge the effects of radiation on markers associated with intestinal stem cells (ISCs) and differentiated epithelial cells. Single cell RNA seq techniques were used to identify shifts in cellular populations FG-4592 and/or radiation treatment of human enteroids. Results: Irradiation produced a signature of enhanced Crypt Base Columnar (CBC) cells and +4 quiescent stem cells markers (Bmi1, Tert, Dclk1) suggesting these specialized cells awaken upon crypt damage and start to proliferate to restore the ISC pool. The +4 cell markers are further enhanced in FG-4592 treated irradiated group, suggesting EGLN inhibition leads to activation of these specialized cell population along with restoration of other intestinal cells like secretory progenitors and Paneth cells. Further, gene set enrichment analysis after FG-4592 treatment showed the activation of key pathways involved in proliferation, maintaining homeostasis, metabolism, and DNA repair that could lead to intestinal proliferation and recovery from radiation damage. Conclusion: Taken together, these preliminary data suggest that HIF stabilization by FG-4592 upregulates the normally quiescent +4 stem cells, a radioresistant stem population historically thought to become active upon radiation injury, along with activation of several other pathways required for normal proliferation and recovery from radiation injury. Our study justifies further exploration in clinical trials as a radioprotective or radio mitigative agent. Citation Format: Neeraj Kumari, Maya Ferrell, Carolina G. Garcia, Cullen M. Taniguchi. Exploring the hypoxia pathway for gastrointestinal radioprotection in human minigut model [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 1107.

Abstract 300: Mechanisms of growth hormone action in the aging tissue microenvironment

Abstract The aging tissue microenvironment undergoes progressive changes enabling age-related pathologies. Senescent cells increase with age, and the secretome released from senescence cells (SASP) affects neighboring cells, often promoting proliferation, tissue inflammation, angiogenesis, and, depending on tissue type, creating a milieu favoring neoplasia. We showed that local non-pituitary growth hormone (GH) accumulates with age in human colon tissue, is induced in response to DNA damage, and suppresses DNA repair. We now show that GH is a SASP component. To examine SASP-derived GH actions on the tissue microenvironment, we co-cultured intact human 3D intestinal organoids with organoids infected with lentivirus expressing either hGH (lentiGH) or vector (lentiV) for 5 weeks. Using whole-exome sequencing to evaluate somatic mutations and somatic copy number alterations, we found that local paracrine GH emanating from lentiGH organoids increases chromosomal instability in intact organoid cells, inducing somatic mutations including deletions, breakends, duplications, and insertions, as compared to organoids co-cultured with lentiV organoids. Mechanisms for chromosomal instability observed in these organoids likely occur as a consequence of GH-induced suppression of DNA damage repair proteins including pATM, pATR, and pBRCA2, leading to DNA damage accumulation, and, in the long run, favoring cell transformation. KEGG pathway analysis of intact organoids subjected to paracrine GH exposure identified changes in focal adhesion pathways (p=0.0016), consistent with observed increased migration, invasion, and anchorage-independent growth of normal human colon cells (hNCC) exposed to GH. Furthermore, IPA analysis revealed EMT pathway changes (p=0.0018),,also confirmed by showing increased EMT transcription factors Twist2 and Snai1 expression.Although senescence has been defined as irreversible proliferative arrest, recent studies now show that senescence can be reversed. Treating hNCC with etoposide to induce senescence and culturing senescent cells in the presence of GH for 10 days resulted in p53 suppression, enabling cells to re-enter the cell cycle, as evidenced by induced Ki67, a marker of proliferation. These post-senescent cells also acquired the stem cell marker SOX2 and exhibited increased Twist2, consistent with anchorage-independent growth and increased migration as compared to senescence cells not treated with GH. These results identify local paracrine GH as an important determinant of the local tissue microenvironment promoting age-associated changes consistent with a pro-neoplastic milieu. Citation Format: Vera Chesnokova, Svetlana Zonis, Tugce Apaydin, Christian Wang, Robert Barrett, Shlomo Melmed. Mechanisms of growth hormone action in the aging tissue microenvironment [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 300.

Abstract 6259: Novel inhibitors of StAR related lipid transfer protein 5 inhibitors target plasma membrane lipid raft growth signaling

Abstract Background: Treatment of colorectal cancer (CRC) presents a major challenge due to chemotherapeutic resistance and recurrence, which are attributed to the presence of cancer stem cells (CSCs). Cholesterol metabolism is a critical regulator of CSCs. Lipid Rafts are cholesterol-rich microdomains in the plasma membrane (PM) that anchor various growth receptors tyrosine kinases (RTKs). STARD5 is a novel protein that helps transport cholesterol from the endoplasmic reticulum to the PM. We have identified specific small molecule inhibitors of the STARD5 which disrupt the lipid rafts, resulting in the inhibition of growth signaling pathways. Methods and Results: In-silico modeling studies using STARD5 crystal structure revealed 8 putative inhibitors (SD5i (A-H)). In vitro binding studies to determine secondary structural changes using circular dichroism spectroscopy revealed SD5iA and SD5iB as excellent STARD5 ligands. Both SD5iA and SD5iB caused a potent inhibition (IC50 0.3 -18 µM) of CSC-enriched 3D spheroids in 9 CRC cell lines representative of 3 consensus molecular subtypes. However, SD5iA but not SD5iB showed toxicity towards normal murine intestinal organoids at effective doses against CRC CSCs. Also, SD5iB enhanced cytotoxicity by oxaliplatin and panitumumab against CRC CSCs in HT-29 spheroids. Hence, SD5iB was advanced into in vivo studies. SD5iB caused no discernible toxicity in doses as high as 100 mg/kg in NCr nude mice at gross, serum chemistry, organ viability, or intestinal stem cell level (organoid formation). Subsequently, we generated s.c. xenograft using dual CSC marker sorted HT-29 cells and enriched them further with chemotherapy (5-fluorouracil and oxaliplatin weekly x 3) treatment followed by randomization to vehicle or SD5iB (100mg/kg i.p. 3/wk x 3 wks.). We observed xenograft growth inhibition and LGR5 expression in SD5iB-treated animals compared to vehicle controls. Mechanistically, we observed a decrease in free accessible PM cholesterol by SD5i measured by fluorescently tagged cholesterol-binding bacterial protein fALOD4 in HT-29 cells. Moreover, lipid raft staining (cholera toxin B staining) was significantly reduced in SD5iB-treated HT-29 cells compared to vehicle control using immunofluorescence. Further, lipid raft isolation was done by sucrose gradient ultracentrifugation to study the changes in the phosphorylation of RTKs SD5iB treatment in HT-29 spheroids resulted in decreased phosphorylation of EGFR, IGF1Rβ, and FGFR1 in isolated lipid rafts. Consequently, we observed a robust inhibition of ERK1/2 activation following SD5iB treatment compared to vehicle control. Conclusion: SD5i shows anti-CSC activity by targeting lipid-raft-driven growth factor signaling. Hence, STARD5 inhibitors represent a novel class of targeted therapy that will enhance the efficacy of FDA-approved therapies in CRC. Citation Format: Shoja Hajira, Chetna Sharon, Daniel RodriguezAgudo, Rio Boothelllo, Glenn Kellogg, Gregorio Gil, William Pandak, Bhaumik B. Patel. Novel inhibitors of StAR related lipid transfer protein 5 inhibitors target plasma membrane lipid raft growth signaling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 6259.

Drug cytotoxicity screening using human intestinal organoids propagated with extensive cost-reduction strategies

Organoids are regarded as physiologically relevant cell models and useful for compound screening for drug development; however, their applications are currently limited because of the high cost of their culture. We previously succeeded in reducing the cost of human intestinal organoid culture using conditioned medium (CM) of L cells co-expressing Wnt3a, R-spondin1, and Noggin. Here, we further reduced the cost by replacing recombinant hepatocyte growth factor with CM. Moreover, we showed that embedding organoids in collagen gel, a more inexpensive matrix than Matrigel, maintains organoid proliferation and marker gene expression similarly when using Matrigel. The combination of these replacements also enabled the organoid-oriented monolayer cell culture. Furthermore, screening thousands of compounds using organoids expanded with the refined method identified several compounds with more selective cytotoxicity against organoid-derived cells than Caco-2 cells. The mechanism of action of one of these compounds, YC-1, was further elucidated. We showed that YC-1 induces apoptosis through the mitogen-activated protein kinase/extracellular signal-regulated kinase pathway, the mechanism of which was distinct from cell death caused by other hit compounds. Our cost-cutting methodology enables large-scale intestinal organoid culture and subsequent compound screening, which could expand the application of intestinal organoids in various research fields.

Fibroblast-derived EGF ligand neuregulin 1 induces fetal-like reprogramming of the intestinal epithelium without supporting tumorigenic growth.

Growth factors secreted by stromal fibroblasts regulate the intestinal epithelium. Stroma-derived epidermal growth factor (EGF) family ligands are implicated in epithelial regeneration and tumorigenesis, but their specific contributions and associated mechanisms remain unclear. Here, we use primary intestinal organoids modeling homeostatic, injured and tumorigenic epithelia to assess how the fibroblast-derived EGF family ligands neuregulin 1 (NRG1) and epiregulin (EREG) regulate the intestinal epithelium. NRG1 was expressed exclusively in the stroma, robustly increased crypt budding and protected intestinal epithelial organoids from radiation-induced damage. NRG1 also induced regenerative features in the epithelium, including a fetal-like transcriptome, suppression of the Lgr5+ stem cell pool and remodeling of the epithelial actin cytoskeleton. Intriguingly, unlike EGF and EREG, NRG1 failed to support the growth of pre-tumorigenic intestinal organoids lacking the tumor suppressor Apc, commonly mutated in human colorectal cancer (CRC). Interestingly, high expression of stromal NRG1 was associated with improved survival in CRC cohorts, suggesting a tumor-suppressive function. Our results highlight the power of stromal NRG1 in transcriptional reprogramming and protection of the intestinal epithelium from radiation injury without promoting tumorigenesis.

Canine Intestinal Organoids as a Novel In Vitro Model of Intestinal Drug Permeability: A Proof-of-Concept Study

Canine Intestinal Organoids as a Novel In Vitro Model of Intestinal Drug Permeability: A Proof-of-Concept Study

A NEW MODEL TO STUDY INTESTINAL FIBROSIS USING IPSC-DERIVED HUMAN EPITHELIAL AND MESENCHYMAL CELLS FROM CROHN’S DISEASE PATIENTS

Intestinal fibrosis is a serious complication of Crohn’s disease (CD) and is caused by the excess deposition of extracellular matrix protein. There are no therapies to prevent or treat this and surgical intervention remains the only treatment option. Numerous cell types, including intestinal epithelial and mesenchymal cells, are implicated in this but research efforts are impaired by a lack of in vitro models. Human intestinal organoids (HIOs), derived from induced pluripotent stem cells (iPSCs), are comprised of both of these cell types; therefore iPSC-derived HIOs represent an approach in which an unlimited number of patient specific cells could be generated for such models. Our goal was to confirm the feasibility of using iPSC-derived epithelial and mesenchymal cells from CD patients to model intestinal fibrosis.

Clinical and Functional Characteristics of the E92K CFTR Gene Variant in the Russian and Turkish Population of People with Cystic Fibrosis

The pathogenic variant E92K (c.274G > A) of the CFTR gene is rare in America and Europe, but it is common for people with cystic fibrosis from Russia and Turkey. We studied the effect of the E92K genetic variant on the CFTR function. The function of the CFTR channel was studied using the intestinal current measurements (ICM) method. The effects of CFTR modulators on the restoration of the CFTR function were studied in the model of intestinal organoids. To assess the effect of E92K on pre-mRNA splicing, the RT-PCR products obtained from patients' intestinal organoid cultures were analyzed. Patients with the genetic variant E92K are characterized by an older age of diagnosis compared to homozygotes F508del and a high frequency of pancreatic sufficiency. The results of the sweat test and the ICM method showed partial preservation of the function of the CFTR channel. Functional analysis of CFTR gene expression revealed a weak effect of the E92K variant on mRNA-CFTR splicing. Lumacaftor (VX-809) has been shown to restore CFTR function in an intestinal organoid model, which allows us to consider the E92K variant as a promising target for therapy with CFTR correctors.

CDK4/6 inhibitor modulating active and quiescent intestinal stem cells for prevention of chemotherapy-induced diarrhea.

Chemotherapy-induced diarrhea causes dehydration, debilitation, infection, and even death, but there are currently no Food and Drug Administration (FDA)-approved drugs for treatment of chemotherapy-induced diarrhea. It is generally believed that the timely regulation of intestinal stem cell (ISC) fate may provide a meaningful solution for intestinal injuries. However, the lineage plasticity of ISCs during and after chemotherapy remains poorly understood. Here, we demonstrated that palbociclib, a cyclin-dependent kinase 4/6 (CDK4/6) inhibitor, regulated the fate of active or quiescent ISCs, provided multilineage protection from the toxicity of several different chemotherapeutics, and accelerated gastrointestinal epithelium recovery. Consistent with in vivo results, we determined that palbociclib enhanced intestinal organoid and ex vivo tissue survival after chemotherapy. Lineage tracing studies have shown that palbociclib protects active ISCs marked by Lgr5 and Olfm4 during chemotherapy and unexpectedly activates quiescent ISCs marked by Bmi1 to immediately participate in crypt regeneration after chemotherapy. Furthermore, palbociclib does not decrease the efficacy of cytotoxic chemotherapy in tumor grafts. The experimental evidence suggests that the combination of CDK4/6 inhibitors with chemotherapy could reduce damage to the gastrointestinal epithelium in patients. © 2023 The Pathological Society of Great Britain and Ireland.

Toward Inclusivity in Preclinical Drug Development: A Proposition to Start with Intestinal Organoids.

Representation of humans from diverse backgrounds in the drug development process is key to advancing health equity, and while clinical trial design has recently made strides toward greater inclusivity, preclinical drug development has struggled to make those same gains. One barrier to inclusion is the current lack of robust and established in vitro model systems that simultaneously capture the complexity of human tissues while representing patient diversity. Here, the use of primary human intestinal organoids as a mechanism to advance inclusive preclinical research is proposed. This in vitro model system not only recapitulates tissue functions and disease states, but also retains the genetic identity and epigenetic signatures of the donors from which they are derived. Thus, intestinal organoids are an ideal in vitro prototype for capturing human diversity. In this perspective, the authors call for an industry-wide effort to leverage intestinal organoids as a starting point to actively and intentionally incorporate diversity into preclinical drug programs.

Personalized medicine: Function of CFTR variant p.Arg334Trp is rescued by currently available CFTR modulators.

Most of the 2,100 CFTR gene variants reported to date are still unknown in terms of their disease liability in Cystic Fibrosis (CF) and their molecular and cellular mechanism that leads to CFTR dysfunction. Since some rare variants may respond to currently approved modulators, characterizing their defect and response to these drugs is essential for effective treatment of people with CF (pwCF) not eligible for the current treatment. Here, we assessed how the rare variant, p.Arg334Trp, impacts on CFTR traffic and function and its response to existing CFTR modulators. To this end, we performed the forskolin-induced swelling (FIS) assay on intestinal organoids from 10 pwCF bearing the p.Arg334Trp variant in one or both alleles of the CFTR gene. In parallel, a novel p.Arg334Trp-CFTR expressing CFBE cell line was generated to characterize the variant individually. Results show that p.Arg334Trp-CFTR does not significantly affect the plasma membrane traffic of CFTR and evidences residual CFTR function. This CFTR variant is rescued by currently available CFTR modulators independently of the variant in the second allele. The study, predicting clinical benefit for CFTR modulators in pwCF with at least one p.Arg334Trp variant, demonstrates the high potential of personalized medicine through theranostics to extend the label of approved drugs for pwCF carrying rare CFTR variants. We recommend that this personalized approach should be considered for drug reimbursement policies by health insurance systems/national health services.

MiRNAs derived from milk small extracellular vesicles inhibit porcine epidemic diarrhea virus infection

Porcine epidemic diarrhea virus (PEDV), a member of the genus Alphacoronavirus in the family Coronaviridae, causes acute diarrhea and/or vomiting, dehydration, and high mortality in neonatal piglets. It has caused huge economic losses to animal husbandry worldwide. Current commercial PEDV vaccines do not provide enough protection against variant and evolved virus strains. No specific drugs are available to treat PEDV infection. The development of more effective therapeutic anti-PEDV agents is urgently needed. Our previous study suggested that porcine milk small extracellular vesicles (sEV) facilitate intestinal tract development and prevent lipopolysaccharide-induced intestinal injury. However, the effects of milk sEV during viral infection remain unclear. Our study found that porcine milk sEV, which was isolated and purified by differential ultracentrifugation, could inhibit PEDV replication in IPEC-J2 and Vero cells. Simultaneously, we constructed a PEDV infection model for piglet intestinal organoids and found that milk sEV also inhibited PEDV infection. Subsequently, in vivo experiments showed that milk sEV pre-feeding exerted robust protection of piglets from PEDV-induced diarrhea and mortality. Strikingly, we found that the miRNAs extracted from milk sEV inhibited PEDV infection. miRNA-seq, bioinformatics analysis, and experimental verification demonstrated that miR-let-7e and miR-27b, which were identified in milk sEV targeted PEDV N and host HMGB1, suppressed viral replication. Taken together, we revealed the biological function of milk sEV in resisting PEDV infection and proved its cargo miRNAs, miR-let-7e and miR-27b, possess antiviral functions. This study is the first description of the novel function of porcine milk sEV in regulating PEDV infection. It provides a better understanding of milk sEV resistance to coronavirus infection, warranting further studies to develop sEV as an attractive antiviral.

Murine colon organoids as a novel model to study Trypanosoma cruzi infection and interactions with the intestinal epithelium.

Chagas disease (CD) is a life-threatening illness caused by the parasite Trypanosoma cruzi (T. cruzi). With around seven million people infected worldwide and over 50,000 deaths per year, CD is a major public health issue in Latin America. The main route of transmission to humans is through a triatomine bug (vector-borne), but congenital and oral transmission have also been reported. The acute phase of CD presents mild symptoms but may develop into a long-lasting chronic illness, characterized by severely impaired cardiac, digestive, and neurological functions. The intestinal tissue appears to have a key role during oral transmission and chronic infection of CD. In this immune-privileged reservoir, dormant/quiescent parasites have been suggested to contribute to disease persistence, infection relapse, and treatment failure. However, the interaction between the intestinal epithelium and T. cruzi has not been examined in depth, in part, due to the lack of in vitro models that approximate to the biological and structural complexity of this tissue. Therefore, to understand the role played by the intestinal tissue during transmission and chronic infection, physiological models resembling the organ complexity are needed. Here we addressed this issue by establishing and characterizing adult stem cell-derived colonoid infection models that are clinically relevant for CD. 3D and 2D systems of murine intestinal organoids infected with T. cruzi Dm28c (a highly virulent strain associated with oral outbreaks) were analyzed at different time points by confocal microscopy. T. cruzi was able to invade and replicate in intestinal epithelial primary cells grown as intact organoids (3D) and monolayers (2D). The permissiveness to pathogen infection differed markedly between organoids and cell lines (primate and intestinal human cell lines). So far, this represents the first evidence of the potential that these cellular systems offer for the study of host-pathogen interactions and the discovery of effective anti-chagasic drugs.

Establishment of Epithelial Inflammatory Injury Model Using Intestinal Organoid Cultures.

Intestinal epithelial dysfunction is critical in the development of inflammatory bowel disease (IBD). However, most cellular experiments related to epithelial barrier studies in IBD have been based on tumor cell line that lack a variety of intestinal epithelial cell types. Thus, intestinal organoids can present the three-dimensional structure and better simulate the physiological structure and function of the intestinal epithelium in vitro. Here, the crypts were isolated from the small intestine of mice; with the participation of major cytokines (EGF, Noggin, and R-Spondin 1 included), the intestinal organoids were established at a density of 100 crypts per well, containing intestinal stem cells (ISC), Paneth cells, goblet cells, and intestinal endocrine cells. We found that tumor necrosis factor-alpha (TNF-α) could induce the inflammatory response of intestinal organoids, and a dose of 10 ng/mL could maintain stable passaging of organoids for dynamic observation. After stimulation with TNF-α, the intestinal organoid cultures showed lower expression of the cell proliferation-related protein identified by monoclonal antibody Ki 67 (Ki67), the ISC marker leucine-rich repeat-containing G protein-coupled receptor 5 (Lgr5), and the intestinal tight junction proteins occludin (Ocln) and claudin-1 (Cldn1) while higher expression of the inflammatory cytokine interleukin- (IL-) 15 and the chemokines C-X-C motif ligand 2 (Cxcl2) and Cxcl10 significantly. In this study, we successfully established an epithelial inflammatory injury model of intestinal organoids, which provides an effective in vitro model for studying the pathogenesis and treatment of IBD.

Ablation of p57+ Quiescent Cancer Stem Cells Suppresses Recurrence After Chemotherapy of Intestinal Tumors.

Quiescent cancer stem cells (CSCs) are resistant to conventional anti-cancer treatments and have been shown to contribute to disease relapse after therapy in some cancer types. The identification and characterization of quiescent CSCs could facilitate the development of strategies to target this cell population and block recurrence. Here, we established a syngeneic orthotopic transplantation model in mice based on intestinal cancer organoids to profile quiescent CSCs. Single-cell transcriptomic analysis of the primary tumors formed in vivo revealed that conventional Lgr5high intestinal CSCs comprise both actively and slowly cycling subpopulations, the latter of which specifically expresses the cyclin-dependent kinase inhibitor p57. Tumorigenicity assays and lineage tracing experiments showed that the quiescent p57+ CSCs contribute in only a limited manner to steady-state tumor growth but they are chemotherapy resistant and drive post-therapeutic cancer recurrence. Ablation of p57+ CSCs suppressed intestinal tumor regrowth after chemotherapy. Together, these results shed light on the heterogeneity of intestinal CSCs and reveal p57+ CSCs as a promising therapeutic target for malignant intestinal cancer.

Stiffness Restricts the Stemness of the Intestinal Stem Cells and Skews Their Differentiation Toward Goblet Cells

Fibrosis and tissue stiffening are hallmarks of inflammatory bowel disease (IBD). We have hypothesized that the increased stiffness directly contributes to the dysregulation of the epithelial cell homeostasis in IBD. Here, we aim to determine the impact of tissue stiffening on the fate and function of the intestinal stem cells (ISCs). We developed a long-term culture system consisting of 2.5-dimensional intestinal organoids grown on a hydrogel matrix with tunable stiffness. Single-cell RNA sequencing provided stiffness-regulated transcriptional signatures of the ISCs and their differentiated progeny. YAP-knockout and YAP-overexpression mice were used to manipulate YAP expression. In addition, we analyzed colon samples from murine colitis models and human IBD samples to assess the impact of stiffness on ISCs invivo. We demonstrated that increasing the stiffness potently reduced the population of LGR5+ ISCs and KI-67+-proliferating cells. Conversely, cells expressing the stem cell marker, olfactomedin-4, became dominant in the crypt-like compartments and pervaded the villus-like regions. Concomitantly, stiffening prompted the ISCs to preferentially differentiate toward goblet cells. Mechanistically, stiffening increased the expression of cytosolic YAP, driving the extension of olfactomedin-4+ cells into the villus-like regions, while it induced the nuclear translocation of YAP, leading to preferential differentiation of ISCs toward goblet cells. Furthermore, analysis of colon samples from murine colitis models and patients with IBD demonstrated cellular and molecular remodeling reminiscent of those observed invitro. Collectively, our findings highlight that matrix stiffness potently regulates the stemness of ISCs and their differentiation trajectory, supporting the hypothesis that fibrosis-induced gut stiffening plays a direct role in epithelial remodeling in IBD.

Tellu - an object-detector algorithm for automatic classification of intestinal organoids.

Intestinal epithelial organoids recapitulate many of the in vivo features of the intestinal epithelium, thus representing excellent research models. Morphology of the organoids based on light-microscopy images is used as a proxy to assess the biological state of the intestinal epithelium. Currently, organoid classification is manual and, therefore, subjective and time consuming, hampering large-scale quantitative analyses. Here, we describe Tellu, an object-detector algorithm trained to classify cultured intestinal organoids. Tellu was trained by manual annotation of >20,000 intestinal organoids to identify cystic non-budding organoids, early organoids, late organoids and spheroids. Tellu can also be used to quantify the relative organoid size, and can classify intestinal organoids into these four subclasses with accuracy comparable to that of trained scientists but is significantly faster and without bias. Tellu is provided as an open, user-friendly online tool to benefit the increasing number of investigations using organoids through fast and unbiased organoid morphology and size analysis.