Alican Özkan

Patients affected by inflammatory bowel disease (IBD) exhibit compromised intestinal barrier function and decreased mucus accumulation, as well as increased inflammation, fibrosis and cancer risk, with symptoms often being exacerbated in women during pregnancy. Here we replicate these IBD hallmarks in human-derived organ-on-a-chip devices lined by colon epithelial cells from individuals with IBD when interfaced with matched fibroblasts, cultured under flow, exposed to peristalsis-like motions and perfused with circulating immune cells. Use of heterotypic tissue recombinants revealed that IBD fibroblasts are the primary drivers of multiple IBD symptoms. In the IBD chip, inflammation and fibrosis are accentuated by peristalsis-like motions and, in female-derived chips, also by exposure to pregnancy-associated hormones. When exposed to carcinogens, the IBD chip shows increased inflammation, gene mutations and chromosome duplication, in contrast to healthy chips. These data suggest that the intestinal stroma, sex hormones and peristalsis-associated mechanical deformations have a key role in driving inflammation, fibrosis and disease progression in male and female individuals with IBD.

Damage to the vascular endothelium is a major contributor to acute radiation injury in multiple organs that underlies acute radiation syndrome (ARS), yet there are no FDA-approved radiation countermeasures targeting endothelial cells. Use of kinome-scale CRISPR screens performed in cultured human vascular endothelial cells isolated from different organs identified CLK2 as a potential radioprotective target. Pharmacological inhibition of CLK2 using TG003 and Cirtuvivint protected these endothelial cells against radiation injury and reversed its effects across the transcriptome and phospho-proteome. Human Organ Chip models of human intestine and lung that contain organ-specific epithelium and microvascular endothelium faithfully replicated clinical features of ARS when exposed to radiation, which were prevented when treated with CLK2 inhibitors. Thus, CLK2 inhibitors may represent a new class of radiation countermeasure drugs that can protect multiple organs against radiation-induced toxicities in patients with ARS.

There is a need for better therapies for acute radiation injury (ARI) of the human intestine as current treatments offer limited efficacy. As the ileum is most sensitive to radiation in patients receiving cancer radiation therapy, we created human Organ Chip microfluidic culture models lined by primary patient-derived ileal epithelial cells interfaced with intestinal microvascular endothelium and exposed them to clinically relevant doses of γ-radiation. These Ileum Chips recapitulated key features of ARI, including cell loss, barrier dysfunction, and inflammation, as well as a therapeutic response to a probiotic formulation (VSL#3) that protects against radiation injury in patients. Use of an AI-enabled drug repurposing algorithm (NemoCAD) with transcriptomic data led to the identification of the antifungal agent miconazole as a potential radiation countermeasure drug, and its protective activity was confirmed on-chip. Combination of AI and human Organ Chip studies may offer a powerful way to repurpose drugs for novel disease applications. Highlights Primary human Organ Chips lined by patient-derived ileal epithelial cells interfaced with intestinal microvascular endothelium faithfully recapitulate acute radiation-induced intestinal injury Use of the Human Ileum Chip in combination with an AI-based drug repurposing platform led to the identification that the FDA approved antifungal drug miconazole has the potential to be rapidly repurposed as a therapeutic countermeasure against acute radiation injury in the human intestine.

Diseases and disorders of dental, oral, and craniofacial (DOC) tissues represent a significant global health burden and have been found to have the greatest age‐standardized prevalence and incidence of all reported diseases worldwide. While the application of novel therapies has been suggested to address the different types of oral health diseases, only a limited number of interventional regenerative therapies have been reported to improve clinical therapeutic outcomes. The lack of novel therapies in DOC tissue regeneration may be in part attributed to the highly resource‐intensive translational path from preclinical models to clinical trials. Recently, stakeholders and regulatory agencies have begun to encourage the use of alternative preclinical models using human tissues for testing therapeutic interventions in place of animal models. This advocacy may provide an opportunity to reduce or eliminate animal testing, ultimately limiting resource expenditure and providing a more efficient regulatory pathway for the approval of novel DOC therapies. While the complexity of DOC physiology, defects, and diseases is not effectively recapitulated in traditional 2D or 3D in vitro culture models, the emergence of more sophisticated in vitro models (or so‐called microphysiological systems that include spheroid, organoid and organ on‐chip (OoC) systems) has enabled effective modeling of clinically simulated disease states in several DOC tissue and organ systems. Here, we aim to provide an overview and collective comparison of these microphysiological systems, outline their current uses in DOC research, and identify important gaps in both their utilization and abilities to recapitulate essential features of native oral‐craniofacial physiology, towards enabling the therapeutic performance of de novo interventions targeted at regeneration outcomes in vivo.

Biofouling and foreign body responses have deleterious effects on the functionality and longevity of implantable biosensors, seriously impeding their implementation for long-term monitoring. Here, we describe a nanocomposite coating composed of a cross-linked lattice of bovine serum albumin and pentaamine-functionalized reduced graphene that is covalently coupled to antibody ligands for analyte detection as well as antibiotic drugs (gentamicin or ceftriaxone), which actively combats biofouling while retaining high electroconductivity and excellent electrochemical immunosensor behavior. Sensors overlaid with this coating inhibit the proliferation of Pseudomonas aeruginosa bacteria and adhesion of primary human fibroblasts while not having any significant effects on fibroblast viability or on the immune function of primary human monocytes. Under these conditions, the sensor maintains its electrochemical stability for at least 3 weeks after exposure to soluble proteins that interfere with the activity of uncoated sensors. Proof-of-concept for the coating’s applicability is demonstrated by integrating the antimicrobial coating within an immunosensor and demonstrating the detection of cytokines in both culture medium and complex human plasma. This new coating technology holds the potential to substantially increase the lifespan of implanted biosensors and widen their application areas, potentially enabling continuous monitoring of analytes in complex biofluids for weeks in vivo.

Inflammatory bowel disease (IBD) patients exhibit compromised intestinal barrier function and decreased mucus accumulation, as well as increased inflammation, fibrosis, and cancer risk, with symptoms often being exacerbated in women during pregnancy. Here, we show that these IBD hallmarks can be replicated using human Organ Chips lined by IBD patient-derived colon epithelial cells interfaced with matched fibroblasts cultured under flow. Use of heterotypic tissue recombinants revealed that IBD fibroblasts are the primary drivers of multiple IBD symptoms. Inflammation and fibrosis are accentuated by peristalsis-like motions in IBD Chips and when exposed to pregnancy-associated hormones in female IBD Chips. Carcinogen exposure also increases inflammation, gene mutations, and chromosome duplication in IBD Chips, but not in Healthy Chips. These data enabled by human Organ Chip technology suggest that the intestinal stroma, sex hormones, and peristalsis-associated mechanical deformations play a key role in driving inflammation, fibrosis, and disease progression in male and female IBD patients.

Alterations in intestinal structure, mechanics and physiology underlie acute and chronic intestinal conditions, many of which are influenced by dysregulation of microbiome, peristalsis, stroma or immune responses. Studying human intestinal physiology or pathophysiology is difficult in preclinical animal models because their microbiomes and immune systems differ from those of humans. Although advances in organoid culture partially overcome this challenge, intestinal organoids still lack crucial features that are necessary to study functions central to intestinal health and disease, such as digestion or fluid flow, as well as contributions from long-term effects of living microbiome, peristalsis and immune cells. Here, we review developments in organ-on-a-chip (organ chip) microfluidic culture models of the human intestine that are lined by epithelial cells and interfaced with other tissues (such as stroma or endothelium), which can experience both fluid flow and peristalsis-like motions. Organ chips offer powerful ways to model intestinal physiology and disease states for various human populations and individual patients, and can be used to gain new insight into underlying molecular and biophysical mechanisms of disease. They can also be used as preclinical tools to discover new drugs and then validate their therapeutic efficacy and safety in the same human-relevant model.

Understanding the effects of inflammation and cirrhosis on the regulation of drug metabolism during the progression of hepatocellular carcinoma (HCC) is critical for developing patient‐specific treatment strategies. Herein, novel 3D vascularized HCC on chips (HCCoCs), composed of HCC, endothelial, stellate, and Kupffer cells tuned to mimic normal or cirrhotic liver stiffness, are created. HCC inflammation is controlled by tuning Kupffer macrophage numbers, and the impact of cytochrome P450‐3A4 (CYP3A4) is investigated by culturing HepG2 HCC cells transfected with CYP3A4 to upregulate expression from baseline. This model allows for the simulation of chemotherapeutic delivery methods such as intravenous injection and transcatheter arterial chemoembolization (TACE). It is shown that upregulation of metabolic activity, incorporation of cirrhosis and inflammation, increases vascular permeability due to upregulated inflammatory cytokines leading to significant variability in chemotherapeutic treatment efficacy. Specifically, it is shown that further modulation of CYP3A4 activity of HCC cells by TACE delivery of doxorubicin provides an additional improvement to treatment response and reduces chemotherapy‐associated endothelial porosity increase. The HCCoCs are shown to have utility in uncovering the impact of the tumor microenvironment during cancer progression on vascular properties, tumor response to therapeutics, and drug delivery strategies.

Understanding the effects of inflammation and cirrhosis on the regulation of drug metabolism during the progression of hepatocellular carcinoma (HCC) is critical for developing patient-specific treatment strategies. In this work, we created novel three-dimensional vascularized HCC-on-a-chips (HCCoC), composed of HCC, endothelial, stellate, and Kupffer cells tuned to mimic normal or cirrhotic liver stiffness. HCC inflammation was controlled by tuning Kupffer macrophage numbers, and the impact of cytochrome P450-3A4 (CYP3A4) was investigated by culturing HepG2 HCC cells transfected with CYP3A4 to upregulate expression from baseline. This model allowed for the simulation of chemotherapeutic delivery methods such as intravenous injection and transcatheter arterial chemoembolization (TACE). We showed that upregulation of metabolic activity, incorporation of cirrhosis and inflammation, increase vascular permeability due to upregulated inflammatory cytokines leading to significant variability in chemotherapeutic treatment efficacy. Specifically, we show that further modulation of CYP3A4 activity of HCC cells by TACE delivery of doxorubicin provides an additional improvement to treatment response and reduces chemotherapy-associated endothelial porosity increase. The HCCoCs were shown to have utility in uncovering the impact of the tumor microenvironment (TME) during cancer progression on vascular properties, tumor response to therapeutics, and drug delivery strategies. Statement of Significance Regulation of drug metabolism during the cancer progression of hepatocellular carcinoma (HCC) can be influential to develop personalized treatment strategies. We created novel vascularized hepatocellular carcinoma-chip (HCCoC) composed of tunable collagen and four main liver-specific cell lines to be used as a preclinical tool. In this model, we found cancer evolution states such as inflammation and cirrhosis increases vascular permeability progressively as a result of increased inflammatory cytokines. Furthermore, delivery of doxorubicin only with embolization improved treatment efficacy by decreasing CYP3A4 activity, which can modulate treatment outcome. Overall, we found different disease states can be influential on CYP3A4, thus its targeting can improve HCC treatment outcome.