Bile salts are key regulators of intestinal homeostasis and host-microbe interactions in the intestine. While bile salt hydrolase (BSH) activity is known to modulate host metabolism, the direct interplay between bile salt signaling, microbial BSH activity, bile acid signaling, and epithelial responses in colorectal cancer remains poorly understood. Here, we established a controlled in vitro co-culture platform using isogenic murine healthy and tumor-derived colon organoids to dissect bile salt-driven epithelial-microbe responses at cellular resolution. We investigated the dynamics between the host and an engineered BSH-expressing Escherichia coli strain (EcAZ-2LsBSH) compared to its native counterpart (EcAZ-2). We found that while bile salts broadly impaired bacterial colonization, EcAZ-2LsBSH preferentially colonized tumor organoids over healthy controls. Crucially, microbial BSH activity functionally rescued host signaling in healthy organoids, driving a robust 1.5-fold upregulation of the farnesoid X receptor (FXR) protein and activating downstream cell lineage pathways. In contrast, tumor organoids exhibited an intrinsic resistance to this FXR-mediated metabolic rescue. Furthermore, we identified the epithelial surface attachment factor Hspg2 (Perlecan) as a dynamically regulated target at the host-microbe interface. While bile salt exposure increased Hspg2 expression, bacterial colonization triggered significant transcriptional suppression, revealing opposing regulatory mechanisms that govern bacterial adhesion. Together, this study demonstrates that microbial metabolism of bile acids exerts profound, context-dependent effects on epithelial signaling and barrier integrity, providing a mechanistic foundation for the development of engineered bacterial therapeutics in colorectal cancer.

Rapid point of care tests for respiratory infections are associated with high rates of false negative results which can drive empiric, and potentially inappropriate, antibiotic use. Because infectious pathogens alter VOC composition, unique VOC signatures in biospecimens hold the potential to discriminate bacterial and viral infections from uninfected controls. One approach for rapid identification of respiratory pathogens is the electronic nose (e-nose), a sensor device that uses artificial intelligence to recognize disease-specific patterns in VOC profiles of gaseous mixtures. In this preclinical proof of concept study, we tested the validity of an e-nose to discriminate PCR-confirmed cases of infection with three viral pathogens (SARS-CoV-2, RSV, influenza A) from uninfected controls using nasopharyngeal test swab media. Using exploratory factor analysis, the e-nose discriminated both influenza A and SAR-CoV-2 from uninfected controls. To assess sensitivity and specificity, we applied factor analysis-based threshold values and obtained high levels of sensitivity (96.30%) and specificity (90.62%) for influenza A and more modest levels for SARS-CoV-2 (sensitivity=75%, specificity=68.57%). We did not apply threshold values to RSV samples because the e-nose sensors showed low discriminatory power for that pathogen. Our findings support proof of concept of the validity of the e-nose to discriminate common viral respiratory pathogens. Our use of binary thresholds for influenza A, which are easily adapted to point-of-care settings, yielded superior sensitivity results and comparable specificity results when compared to rapid tests. We recommend that future studies apply our analytic approach to samples of human breath to determine if these findings can be replicated or improved.

Bile salts are key regulators of host microbe interactions and epithelial signaling in the intestine. Gut bacteria can deconjugate primary bile salts, which can be leveraged to engineer targeted therapies through bile salt hydrolase (BSH) activity. However, the interplay between bile salt signaling, microbial metabolism, and tumor-associated colonization remains poorly understood. Here, we establish an in vitro colon organoid platform to dissect bile salt driven epithelial microbe dynamics at cellular resolution. Using this system, we found that bile salts markedly modulated colonization of native Escherichia coli (EcAZ-2) and a BSH-expressing strain (EcAZ-2LsBSH) in healthy versus tumor murine organoids. Under bile salt exposure, EcAZ-2LsBSH preferentially colonized tumor organoids, though overall colonization was lower than that of the non-BSH strain. Beyond effects on bacterial colonization, bile salts also directly activated host signaling pathways. In presence of bile salts, EcAZ-2LsBSH significantly enhanced activation of bile acid receptors such as farnesoid X receptor (FXR) by 2-fold in healthy organoids. These findings reveal a mechanistic bridge between in vivo microbial function and bile salt interactions, offering potential microbiota and bile acid targeted therapeutic strategies.

[This corrects the article DOI: 10.1371/journal.pone.0332399.].

Despite an overall decrease in occurrence, colorectal cancer (CRC) remains the third most common cause of cancer deaths in the USA. Detection of CRC is difficult in high-risk groups, including those with genetic predispositions, with disease traits, or from certain demographics. There is emerging interest in using engineered bacteria to identify early CRC development, monitor changes in the adenoma and CRC microenvironment, and prevent cancer progression. Novel genetic circuits for cancer therapeutics or functions to enhance existing treatment modalities have been tested and verified in vitro and in vivo. Inclusion of biocontainment measures would prepare strains to meet therapeutic standards. Thus, engineered bacteria present an opportunity for detection and treatment of CRC lesions in a highly sensitive and specific manner.

Organ-on-chip (OOC) technology has gained importance for biomedical studies and drug development. This technology involves microfluidic devices that mimic the structure and function of specific human organs or tissues. OOCs are a promising alternative to traditional cell-based models and animals, as they provide a more representative experimental model of human physiology. By creating a microenvironment that closely resembles in vivo conditions, OOC platforms enable the study of intricate interactions between different cells as well as a better understanding of the underlying mechanisms pertaining to diseases. OOCs can be integrated with other technologies, such as sensors and imaging systems to monitor real-time responses and gather extensive data on tissue behavior. Despite these advances, OOCs for many organs are in their initial stages of development, with several challenges yet to be overcome. These include improving the complexity and maturity of these cellular models, enhancing their reproducibility, standardization, and scaling them up for high-throughput uses. Nonetheless, OOCs hold great promise in advancing biomedical research, drug discovery, and personalized medicine, benefiting human health and well-being. Here, we review several recent OOCs that attempt to overcome some of these challenges. These OOCs with unique applications can be engineered to model organ systems such as the stomach, cornea, blood vessels, and mouth, allowing for analyses and investigations under more realistic conditions. With this, these models can lead to the discovery of potential therapeutic interventions. In this review, we express the significance of the relationship between mucosal tissues and vasculature in organ-on-chip (OOC) systems. This interconnection mirrors the intricate physiological interactions observed in the human body, making it crucial for achieving accurate and meaningful representations of biological processes within OOC models. Vasculature delivers essential nutrients and oxygen to mucosal tissues, ensuring their proper function and survival. This exchange is critical for maintaining the health and integrity of mucosal barriers. This review will discuss the OOCs used to represent the mucosal architecture and vasculature, and it can encourage us to think of ways in which the integration of both can better mimic the complexities of biological systems and gain deeper insights into various physiological and pathological processes. This will help to facilitate the development of more accurate predictive models, which are invaluable for advancing our understanding of disease mechanisms and developing novel therapeutic interventions.

Analysis of volatile organic compounds (VOCs) in breath specimens has potential for point of care (POC) screening due to ease of sample collection. While the electronic nose (e-nose) is a standard VOC measure across a wide range of industries, it has not been adopted for POC screening in healthcare. One limitation of the e-nose is the absence of mathematical models of data analysis that yield easily interpreted findings at POC. The purposes of this review were to (1) examine the sensitivity/specificity results from studies that analyzed breath smellprints using the Cyranose 320, a widely used commercial e-nose, and (2) determine whether linear or nonlinear mathematical models are superior for analyzing Cyranose 320 breath smellprints. This systematic review was conducted according to the guidelines of the Preferred Reporting Items for Systematic Review and Meta-Analyses using keywords related to e-nose and breath. Twenty-two articles met the eligibility criteria. Two studies used a linear model while the rest used nonlinear models. The two studies that used a linear model had a smaller range for mean of sensitivity and higher mean (71.0%-96.0%;M= 83.5%) compared to the studies that used nonlinear models (46.9%-100%;M= 77.0%). Additionally, studies that used linear models had a smaller range for mean of specificity and higher mean (83.0%-91.5%;M= 87.2%) compared to studies that used nonlinear models (56.9%-94.0%;M= 76.9%). Linear models achieved smaller ranges for means of sensitivity and specificity compared to nonlinear models supporting additional investigations of their use for POC testing. Because our findings were derived from studies of heterogenous medical conditions, it is not known if they generalize to specific diagnoses.

Collective cell behavior contributes to all stages of cancer progression. Understanding how collective behavior emerges through cell-cell interactions and decision-making will advance our understanding of cancer biology and provide new therapeutic approaches. Here, we summarize an interdisciplinary discussion on multicellular behavior in cancer, draw lessons from other scientific disciplines, and identify future directions.

A variety of volatile organic compounds (VOCs) are produced and emitted by the human body every day. The identity and concentration of these VOCs reflect an individual’s metabolic condition. Information regarding the production and origin of VOCs, however, has yet to be congruent among the scientific community. This review article focuses on the recent investigations of the source and detection of biological VOCs as a potential for noninvasive discrimination between healthy and diseased individuals. Analyzing the changes in the components of VOC profiles could provide information regarding the molecular mechanisms behind disease as well as presenting new approaches for personalized screening and diagnosis. VOC research has prioritized the study of cancer, resulting in many research articles and reviews being written on the topic. This review summarizes the information gained about VOC cancer studies over the past 10 years and looks at how this knowledge correlates with and can be expanded to new and upcoming fields of VOC research, including neurodegenerative and other noninfectious diseases. Recent advances in analytical techniques have allowed for the analysis of VOCs measured in breath, urine, blood, feces, and skin. New diagnostic approaches founded on sensor-based techniques allow for cheaper and quicker results, and we compare their diagnostic dependability with gas chromatography- and mass spectrometry-based techniques. The future of VOC analysis as a clinical practice and the challenges associated with this transition are also discussed and future research priorities are summarized.

The patient population suffering from pancreatic ductal adenocarcinoma (PDAC) presents, as a whole, with a high degree of molecular tumor heterogeneity. The heterogeneity of PDAC tumor composition has complicated treatment and stalled success in clinical trials. Current in vitro techniques insufficiently replicate the intricate stromal components of PDAC tumor microenvironments (TMEs) and fail to model a given tumor’s unique genetic phenotype. The development of patient-derived organoids (PDOs) has opened the door for improved personalized medicine since PDOs are derived directly from patient tumors, thus preserving the tumors’ unique behaviors and genetic phenotypes. This study developed a tumor-chip device engineered to mimic the PDAC TME by incorporating PDOs and stromal cells, specifically pancreatic stellate cells and macrophages. Establishing PDOs in a multicellular microfluidic chip device prolongs cellular function and longevity and successfully establishes a complex organotypic tumor environment that incorporates desmoplastic stroma and immune cells. When primary cancer cells in monoculture were subjected to stroma-depleting agents, there was no effect on cancer cell viability. However, targeting stroma in our tumor-chip model resulted in a significant increase in the chemotherapy effect on cancer cells, thus validating the use of this tumor-chip device for drug testing.

Life on Earth depends on oxygen; human tissues require oxygen signaling, whereas many microorganisms, including bacteria, thrive in anoxic environments. Despite these differences, human tissues and bacteria coexist in close proximity to each other such as in the intestine. How oxygen governs intestinal-bacterial interactions remains poorly understood. To address to this gap, we created a dual-oxygen environment in a microfluidic device to study the role of oxygen in regulating the regulation of intestinal enzymes and proteins by gut bacteria. Two-layer microfluidic devices were designed using a fluid transport model and fabricated using soft lithography. An oxygen-sensitive material was integrated to determine the oxygen levels. The intestinal cells were cultured in the upper chamber of the device. The cells were differentiated, upon which bacterial strains, a facultative anaerobe, Escherichia coli Nissle 1917, and an obligate anaerobe, Bifidobacterium Adolescentis, were cultured with the intestinal cells. The microfluidic device successfully established a dual-oxygen environment. Of particular importance in our findings was that both strains significantly upregulated mucin proteins and modulated several intestinal transporters and transcription factors but only under the anoxic–oxic oxygen gradient, thus providing evidence of the role of oxygen on bacterial-epithelial signaling. Our work that integrates cell and molecular biology with bioengineering presents a novel strategy to engineer an accessible experimental system to provide tailored oxygenated environments. The work could provide new avenues to study intestine-microbiome signaling and intestinal tissue engineering, as well as a novel perspective on the indirect effects of gut bacteria on tissues including tumors.

The coronavirus disease 2019 (COVID-19) pandemic began in January 2020 in Wuhan, China, with a new coronavirus designated SARS-CoV-2. The principal cause of death from COVID-19 disease quickly emerged as acute respiratory distress syndrome (ARDS). A key ARDS pathogenic mechanism is the “Cytokine Storm”, which is a dramatic increase in inflammatory cytokines in the blood. In the last two years of the pandemic, a new pathology has emerged in some COVID-19 survivors, in which a variety of long-term symptoms occur, a condition called post-acute sequelae of COVID-19 (PASC) or “Long COVID”. Therefore, there is an urgent need to better understand the mechanisms of the virus. The spike protein on the surface of the virus is composed of joined S1–S2 subunits. Upon S1 binding to the ACE2 receptor on human cells, the S1 subunit is cleaved and the S2 subunit mediates the entry of the virus. The S1 protein is then released into the blood, which might be one of the pivotal triggers for the initiation and/or perpetuation of the cytokine storm. In this study, we tested the hypothesis that the S1 spike protein is sufficient to activate inflammatory signaling and cytokine production, independent of the virus. Our data support a possible role for the S1 spike protein in the activation of inflammatory signaling and cytokine production in human lung and intestinal epithelial cells in culture. These data support a potential role for the SARS-CoV-2 S1 spike protein in COVID-19 pathogenesis and PASC.

The development of hepatic insulin resistance (IR) is a critical factor in developing type 2 diabetes (T2D), where insulin fails to inhibit hepatic glucose production but retains its capacity to promote hepatic de novo lipogenesis leading to hyperglycemia and hypertriglyceridemia. Improving insulin sensitivity can be effective in preventing and treating T2D. However, selective control of glucose and lipid synthesis has been difficult. It is known that excess white adipose tissue is detrimental to insulin sensitivity, whereas brown adipose tissue transplantation can restore it in diabetic mice. However, challenges remain in our understanding of liver-adipose communication because the confounding effects of hypothalamic regulation of metabolic function cannot be ruled out in previous studies. There is a lack of in vitro models that use primary cells to study cellular-crosstalk under insulin resistant conditions. Building upon our previous work on the microfluidic primary liver and adipose organ-on-chips, we report for the first time, the development of an integrated insulin resistant liver-adipose (white and brown) organ-on-chip. The design of the microfluidic device was carried out using computational fluid dynamics; the experimental studies were conducted by carrying out detailed biochemical analysis RNA-seq analysis on both cell types. Further, we tested the hypothesis that brown adipocytes (BAC) regulated both hepatic insulin sensitivity and de novo lipogenesis. Our results show that BAC effectively restored insulin sensitivity and supressed hepatic glucose production and de novo lipogenesis suggesting that the experimental platform could be useful for identifying potential therapeutics to treat IR and diabetes.

An accurate in vitro model of human adipose tissue could assist in the study of adipocyte function and allow for better tools for screening new therapeutic compounds. Cell culture models on two-dimensional surfaces fall short of mimicking the three-dimensional in vivo adipose environment, while three-dimensional culture models are often unable to support long-term cell culture due, in part, to insufficient mass transport. Microfluidic systems have been explored for adipose tissue models. However, current systems have primarily focused on 2D cultured adipocytes. In this work, a 3D human adipose microtissue was engineered within a microfluidic system. Human adipose-derived stem cells (ADSCs) were used as the cell source for generating differentiated adipocytes. The ADSCs differentiated within the microfluidic system formed a dense lipid-loaded mass with the expression of adipose tissue genetic markers. Engineered adipose tissue showed a decreased adiponectin secretion and increased free fatty acid secretion with increasing shear stress. Adipogenesis markers were downregulated with increasing shear stress. Overall, this microfluidic system enables the on-chip differentiation and development of a functional 3D human adipose microtissue supported by the interstitial flow. This system could potentially serve as a platform for in vitro drug testing for adipose tissue-related diseases.

Pancreatic Ductal Adenocarcinoma (PDAC) is an expeditiously fatal malignancy with a five-year survival rate of 6–8%. Conventional chemotherapeutics fail in many cases due to inadequate primary response and rapidly developing resistance. This treatment failure is particularly challenging in pancreatic cancer because of the high molecular heterogeneity across tumors. Additionally, a rich fibro-inflammatory component within the tumor microenvironment (TME) limits the delivery and effectiveness of anticancer drugs, further contributing to the lack of response or developing resistance to conventional approaches in this cancer. As a result, there is an urgent need to model pancreatic cancer ex vivo to discover effective drug regimens, including those targeting the components of the TME on an individualized basis. Patient-derived three-dimensional (3D) organoid technology has provided a unique opportunity to study patient-specific cancerous epithelium. Patient-derived organoids cultured with the TME components can more accurately reflect the in vivo tumor environment. Here we present the advances in organoid technology and multicellular platforms that could allow for the development of “organ-on-a-chip” approaches to recapitulate the complex cellular interactions in PDAC tumors. We highlight the current advances of the organ-on-a-chip-based cancer models and discuss their potential for the preclinical selection of individualized treatment in PDAC.

The intestinal environment is unique because it supports the intestinal epithelial cells under a normal oxygen environment and the microbiota under an anoxic environment. Due to importance of understanding the interactions between the epithelium and the microbiota, there is a strong need for developing representative and simple experimental models. Current approaches do not capture the partitioned oxygen environment, require external anaerobic chambers, or are complex. Another major limitation is that with the solutions that can mimic this oxygen environment, the oxygenation level of the epithelial cells is not known, raising the question whether the cells are hypoxic or not. We report standalone microfluidic devices that form a partitioned oxygen environment without the use of an external anaerobic chamber or oxygen scavengers to coculture intestinal epithelial and bacterial cells. By changing the thickness of the device cover, the oxygen tension in the chamber was modulated. We verified the oxygen levels using several tests: microscale oxygen sensitive sensors which were integrated within the devices, immunostaining of Caco-2 cells to determine hypoxia levels, and genetically encoded bacteria to visualize the growth. Collectively, these methods monitored oxygen concentrations in the devices more comprehensively than previous reports and allowed for control of oxygen tension to match the requirements of both intestinal cells and anaerobic bacteria. Our experimental model is supported by the mathematical model that considered diffusion of oxygen into the top chamber. This allowed us to experimentally determine the oxygen consumption rate of the intestinal epithelial cells under perfusion.

Metabolism of glucose and lipids is essential for nutrient balance and metabolic homeostasis, and is dynamically regulated by adipose tissue and liver. Dysfunction in regulation of these molecules as well as the secreted factors results in metabolic syndrome and insulin resistance (IR), which is a precursor to type 2 diabetes. Studies have shown that as the main site of adaptive thermogenesis, brown adipose tissue (BAT) improves hepatic insulin sensitivity, whereas white adipose tissue (WAT) can induce hepatic IR. However, how these organs communicate to regulate insulin sensitivity is not completely understood due to the lack of representative experimental models. Animals models are useful but suffer from confounding effects from other organs; traditional in vitro models have limited physiological representation. We have developed an organ-on-chip platform to study the interactions between BAT/WAT and liver under different metabolic states. The adipose-liver organ-chip consists of two interconnected microfluidic devices - brown/white adipocytes were cultured in one device and hepatocytes (insulin sensitive and IR) in the other, both under perfusion. We show that (a) adipocytes exhibited higher intracellular lipid and fatty acid secretion and (b) the hepatocytes secreted higher albumin compared to traditional co-cultures. We found that brown adipocytes secretions restored insulin sensitivity, and improved glucose/lipid metabolism in IR hepatocytes. In contrast, white adipocytes worsened insulin sensitivity and glucose/lipid metabolism. IR hepatocytes lowered Akt-phosphorylation and glucose uptake while upregulated adipocyte fatty acids secretion. Through RNA-seq, we have identified adipose genes responsible for improving hepatic IR. We have discovered potential new targets for improving hepatic insulin sensitivity. The novel organ-chip platform represented the cells physiologically and will be useful in the discovery and validation of new therapeutic targets for T2D. Disclosure N. Tanataweethum: None. A. Trang: None. L. Annepureddy: None. J. Mehta: None. R.N. Cohen: None. A. Bhushan: None. Funding DRTC (P30DK020595)