Reproducibility and robustness of high-throughput S1500+ transcriptomics on primary rat hepatocytes for chemical-induced hepatotoxicity assessment.

Cell-based in vitro models coupled with high-throughput transcriptomics (HTTr) are increasingly utilized as alternative methods to animal-based toxicity testing. Here, using a panel of 14 chemicals with different risks of human drug-induced liver injury (DILI) and two dosing concentrations, we evaluated an HTTr platform comprised of collagen sandwich primary rat hepatocyte culture and the TempO-Seq surrogate S1500+ (ST) assay. First, the HTTr platform was found to exhibit high reproducibility between technical and biological replicates (r greater than 0.85). Connectivity mapping analysis further demonstrated a high level of inter-platform reproducibility between TempO-Seq data and Affymetrix GeneChip data from the Open TG-GATES project. Second, the TempO-Seq ST assay was shown to be a robust surrogate to the whole transcriptome (WT) assay in capturing chemical-induced changes in gene expression, as evident from correlation analysis, PCA and unsupervised hierarchical clustering. Gene set enrichment analysis (GSEA) using the Hallmark gene set collection also demonstrated consistency in enrichment scores between ST and WT assays. Lastly, unsupervised hierarchical clustering of hallmark enrichment scores broadly divided the samples into hepatotoxic, intermediate, and non-hepatotoxic groups. Xenobiotic metabolism, bile acid metabolism, apoptosis, p53 pathway, and coagulation were found to be the key hallmarks driving the clustering. Taken together, our results established the reproducibility and performance of collagen sandwich culture in combination with TempO-Seq S1500+ assay, and demonstrated the utility of GSEA using the hallmark gene set collection to identify potential hepatotoxicants for further validation.

Isolation of Primary Rat Hepatocytes with Multiparameter Perfusion Control.

Primary hepatocytes are widely used in basic research on liver diseases and for toxicity testing in vitro. The two-step collagenase perfusion procedure for primary hepatocyte isolation is technically challenging, especially in portal vein cannulation. The procedure is also prone to occasional contamination and variations in perfusion conditions due to difficulties in the assembly, optimization, or maintenance of the perfusion setup. Here, a detailed protocol for an improved two-step collagenase perfusion procedure with multiparameter perfusion control is presented. Primary rat hepatocytes were successfully and reliably isolated by taking the necessary technical precautions at critical steps of the procedure, and by reducing the operational difficulty and mitigating the variability of perfusion parameters through the adoption of a special intravenous catheter, standardized sterile disposable tubing, temperature control, and real-time monitoring and alarm system. The isolated primary rat hepatocytes consistently exhibit high cell viability (85%-95%), yield (2-5 x 108 cells per 200-300 g rat) and functionality (albumin, urea and CYP activity). The procedure was complemented by an integrated perfusion system, which is compact enough to be set up in the laminar flow hood to ensure aseptic operation.

Artificial intelligence-enhanced white-light colonoscopy with attention guidance predicts colorectal cancer invasion depth.

BACKGROUND AND AIMS: Endoscopic submucosal dissection (ESD) and EMR are applied in treating superficial colorectal neoplasms but are contraindicated by deeply invasive colorectal cancer (CRC). The invasion depth of neoplasms can be examined by an automated artificial intelligence (AI) system to determine the applicability of ESD and EMR. METHODS: A deep convolutional neural network with a tumor localization branch to guide invasion depth classification was constructed on the GoogLeNet architecture. The model was trained using 7734 nonmagnified white-light colonoscopy (WLC) images supplemented by image augmentation from 657 lesions labeled with histopathologic analysis of invasion depth. An independent testing dataset consisting of 1634 WLC images from 156 lesions was used to validate the model. RESULTS: For predicting noninvasive and superficially invasive neoplasms, the model achieved an overall accuracy of 91.1% (95% confidence interval [CI], 89.6%-92.4%), with 91.2% sensitivity (95% CI, 88.8%-93.3%) and 91.0% specificity (95% CI, 89.0%-92.7%) at an optimal cutoff of .41 and the area under the receiver operating characteristic (AUROC) curve of .970 (95% CI, .962-.978). Inclusion of the advanced CRC data significantly increased the sensitivity in differentiating superficial neoplasms from deeply invasive early CRC to 65.3% (95% CI, 61.9%-68.8%) with an AUROC curve of .729 (95% CI, .699-.759), similar to experienced endoscopists (.691; 95% CI, .624-.758). CONCLUSIONS: We have developed an AI-enhanced attention-guided WLC system that differentiates noninvasive or superficially submucosal invasive neoplasms from deeply invasive CRC with high accuracy, sensitivity, and specificity.

Bile canaliculi contract autonomously by releasing calcium into hepatocytes via mechanosensitive calcium channel.

Drug-induced hepatocellular cholestasis leads to altered bile flow. Bile is propelled along the bile canaliculi (BC) by actomyosin contractility, triggered by increased intracellular calcium (Ca2+). However, the source of increased intracellular Ca2+ and its relationship to transporter activity remains elusive. We identify the source of the intracellular Ca2+ involved in triggering BC contractions, and we elucidate how biliary pressure regulates Ca2+ homeostasis and associated BC contractions. Primary rat hepatocytes were cultured in collagen sandwich. Intra-canalicular Ca2+ was measured with fluo-8; and intra-cellular Ca2+ was measured with GCaMP. Pharmacological modulators of canonical Ca2+-channels were used to study the Ca2+-mediated regulation of BC contraction. BC contraction correlates with cyclic transfer of Ca2+ from BC to adjacent hepatocytes, and not with endoplasmic reticulum Ca2+. A mechanosensitive Ca2+ channel (MCC), Piezo-1, is preferentially localized at BC membranes. The Piezo-1 inhibitor GsMTx-4 blocks the Ca2+ transfer, resulting in cholestatic generation of BC-derived vesicles whereas Piezo-1 hyper-activation by Yoda1 increases the frequency of Ca2+ transfer and BC contraction cycles. Yoda1 can recover normal BC contractility in drug-induced hepatocellular cholestasis, supporting that Piezo-1 regulates BC contraction cycles. Finally, we show that hyper-activating Piezo-1 can be exploited to normalize bile flow in drug-induced hepatocellular cholestasis.

Biomimetic niches reveal the minimal cues to trigger apical lumen formation in single hepatocytes.

The symmetry breaking of protein distribution and cytoskeleton organization is an essential aspect for the development of apicobasal polarity. In embryonic cells this process is largely cell autonomous, while differentiated epithelial cells collectively polarize during epithelium formation. Here, we demonstrate that the de novo polarization of mature hepatocytes does not require the synchronized development of apical poles on neighbouring cells. De novo polarization at the single-cell level by mere contact with the extracellular matrix and immobilized cadherin defining a polarizing axis. The creation of these single-cell liver hemi-canaliculi allows unprecedented imaging resolution and control and over the lumenogenesis process. We show that the density and localization of cadherins along the initial cell-cell contact act as key triggers of the reorganization from lateral to apical actin cortex. The minimal cues necessary to trigger the polarization of hepatocytes enable them to develop asymmetric lumens with ectopic epithelial cells originating from the kidney, breast or colon.

Mechanosensing in liver regeneration.

Liver is highly regenerative as it can restore its function and size even after 70% partial hepatectomy. During liver regeneration, the mechanical and chemical environment of liver is altered with accumulation of various growth factors and remodeling of extracellular environment. Cells can sense the changes in their cellular environment through various chemo and mechanosensors present on their surfaces. These changes are then transduced by initiation of multiple signaling pathways. Traditional view of liver regeneration describes the process as a cascade of chemical signaling pathways. In this review, we describe the role of mechanical forces and mechanosensing in regulating liver regeneration with focus on the role of altered shear and extracellular matrix environment following injury. These mechanosensing mechanisms either generate molecular signals that further activate downstream signaling pathways such as YAP or directly transduce mechanical signals by regulating actomyosin cytoskeleton. These signals travel to the decision center such as nucleus to switch cell fate and activate functions needed in liver regeneration, e.g. proliferation of various hepatic cell types, differentiation of hepatic stem cells, extracellular matrix remodeling and termination signals that regulate the regenerated liver size. Different mechanical and chemical signals coordinate intracellular chemical signaling pathways leading to robust liver regeneration.

Actomyosin contractility drives bile regurgitation as an early response during obstructive cholestasis.

BACKGROUND & AIMS: A wide range of liver diseases manifest as biliary obstruction, or cholestasis. However, the sequence of molecular events triggered as part of the early hepatocellular homeostatic response in obstructive cholestasis is poorly elucidated. Pericanalicular actin is known to accumulate during obstructive cholestasis. Therefore, we hypothesized that the pericanalicular actin cortex undergoes significant remodeling as a regulatory response to obstructive cholestasis. METHODS: In vivo investigations were performed in a bile duct-ligated mouse model. Actomyosin contractility was assessed using sandwich-cultured rat hepatocytes transfected with various fluorescently labeled proteins and pharmacological inhibitors of actomyosin contractility. RESULTS: Actomyosin contractility induces transient deformations along the canalicular membrane, a process we have termed inward blebbing. We show that these membrane intrusions are initiated by local ruptures in the pericanalicular actin cortex; and they typically retract following repair by actin polymerization and actomyosin contraction. However, above a certain osmotic pressure threshold, these inward blebs pinch away from the canalicular membrane into the hepatocyte cytoplasm as large vesicles (2-8µm). Importantly, we show that these vesicles aid in the regurgitation of bile from the bile canaliculi. CONCLUSION: Actomyosin contractility induces the formation of bile-regurgitative vesicles, thus serving as an early homeostatic mechanism against increased biliary pressure during cholestasis. LAY SUMMARY: Bile canaliculi expand and contract in response to the amount of secreted bile, and resistance from the surrounding actin bundles. Further expansion due to bile duct blockade leads to the formation of inward blebs, which carry away excess bile to prevent bile build up in the canaliculi.

Kinectin-dependent ER transport supports the focal complex maturation required for chemotaxis in shallow gradients.

Chemotaxis in shallow gradients of chemoattractants is accomplished by preferential maintenance of protrusions oriented towards the chemoattractant; however, the mechanism of preferential maintenance is not known. Here, we test the hypothesis that kinectin-dependent endoplasmic reticulum (ER) transport supports focal complex maturation to preferentially maintain correctly oriented protrusions. We knocked down kinectin expression in MDA-MB-231 cells using small interfering RNA and observed that kinectin contributes to the directional bias, but not the speed, of cell migration. Kymograph analysis revealed that the extension of protrusions oriented towards the chemoattractant was not affected by kinectin knockdown, but that their maintenance was. Immunofluorescence staining and live-cell imaging demonstrated that kinectin transports ER preferentially to protrusions oriented towards the chemoattractant. ER then promotes the maturation of focal complexes into focal adhesions to maintain these protrusions for chemotaxis. Our results show that kinectin-dependent ER distribution can be localized by chemoattractants and provide a mechanism for biased protrusion choices during chemotaxis in shallow gradients of chemoattractants.

The self-limiting dynamics of TGF-ß signaling in silico and in vitro, with negative feedback through PPM1A upregulation.

The TGF-ß/Smad signaling system decreases its activity through strong negative regulation. Several molecular mechanisms of negative regulation have been published, but the relative impact of each mechanism on the overall system is unknown. In this work, we used computational and experimental methods to assess multiple negative regulatory effects on Smad signaling in HaCaT cells. Previously reported negative regulatory effects were classified by time-scale: degradation of phosphorylated R-Smad and I-Smad-induced receptor degradation were slow-mode effects, and dephosphorylation of R-Smad was a fast-mode effect. We modeled combinations of these effects, but found no combination capable of explaining the observed dynamics of TGF-ß/Smad signaling. We then proposed a negative feedback loop with upregulation of the phosphatase PPM1A. The resulting model was able to explain the dynamics of Smad signaling, under both short and long exposures to TGF-ß. Consistent with this model, immuno-blots showed PPM1A levels to be significantly increased within 30 min after TGF-ß stimulation. Lastly, our model was able to resolve an apparent contradiction in the published literature, concerning the dynamics of phosphorylated R-Smad degradation. We conclude that the dynamics of Smad negative regulation cannot be explained by the negative regulatory effects that had previously been modeled, and we provide evidence for a new negative feedback loop through PPM1A upregulation. This work shows that tight coupling of computational and experiments approaches can yield improved understanding of complex pathways.