A new strategy for screening novel functional genes involved in reduction of lipid droplet accumulation.

Lipid droplets (LDs) are organelles that store excess lipids and provide fatty acids for energy production during starvation. LDs are also essential for cellular maintenance, but excessive accumulation of LDs triggers various cancers in addition to metabolic diseases such as diabetes. In this study, we aimed to develop a strategy to identify new genes that reduces accumulation of LDs in cancer cells using an RNA interference (RNAi) screening system employing artificial sequence-enriched shRNA libraries. Monitoring LDs by fluorescent activated cell sorting, the subsequently collected cumulative LDs cells, and shRNA sequence analysis identified a clone that potentially functioned to accumulate LDs. The clone showed no identical sequence to human Refseq. It showed very similar sequence to seven genes by allowing three mismatches. Among these genes, we identified the mediator complex subunit 6 (MED6) gene as a target of this shRNA. Silencing of MED6 led to an increase in LD accumulation and expression of the marker genes, PLIN2 and DGAT1, in fatty cells. MED6 is a member of the mediator complex that regulates RNA polymerase II transcription through transcription factor II. Some mediator complexes play important roles in both normal and pathophysiological transcription processes. These results suggest that MED6 transcriptionally regulates the genes involved in lipid metabolism and suppresses LD accumulation.

ER Stress Decreases Gene Expression Of Transmembrane Protein 117 Via Activation of PKR-like ER Kinase.

Stress response is an inherent mechanism in the endoplasmic reticulum (ER). The inducers of ER cause a specific cascade of reactions, leading to gene expression. Transmembrane protein 117 (TMEM117) is in the ER and plasma membrane. In our previous study, TMEM117 protein expression was found to be decreased by an ER stress inducer. However, the mechanism underlying this decrease in TMEM117 protein expression remains unclear. This study aimed to elucidate the mechanism underlying the decrease in TMEM117 protein expression during ER stress and identify the unfolded protein response (UPR) pathway related to decreased TMEM117 protein expression. We showed that the gene expression levels of TMEM117 were decreased by ER stress inducers and were regulated by PKR-like ER kinase (PERK), indicating that TMEM117 protein expression was regulated by the signaling pathway. Surprisingly, gene knockdown of activating transcription factor 4 (ATF4) downstream of PERK did not affect the gene expression of TMEM117. These results suggest that TMEM117 protein expression during ER stress is transcriptionally regulated by PERK but not by ATF4. TMEM117 has a potential to be a new therapeutic target against ER stress-related diseases.

Deep Learning of Phase-Contrast Images of Cancer Stem Cells Using a Selected Dataset of High Accuracy Value Using Conditional Generative Adversarial Networks.

Artificial intelligence (AI) technology for image recognition has the potential to identify cancer stem cells (CSCs) in cultures and tissues. CSCs play an important role in the development and relapse of tumors. Although the characteristics of CSCs have been extensively studied, their morphological features remain elusive. The attempt to obtain an AI model identifying CSCs in culture showed the importance of images from spatially and temporally grown cultures of CSCs for deep learning to improve accuracy, but was insufficient. This study aimed to identify a process that is significantly efficient in increasing the accuracy values of the AI model output for predicting CSCs from phase-contrast images. An AI model of conditional generative adversarial network (CGAN) image translation for CSC identification predicted CSCs with various accuracy levels, and convolutional neural network classification of CSC phase-contrast images showed variation in the images. The accuracy of the AI model of CGAN image translation was increased by the AI model built by deep learning of selected CSC images with high accuracy previously calculated by another AI model. The workflow of building an AI model based on CGAN image translation could be useful for the AI prediction of CSCs.

Effects of the anti-inflammatory drug celecoxib on cell death signaling in human colon cancer.

The anti-inflammatory drug celecoxib, the only inhibitor of cyclooxygenase-2 (COX-2) with anticancer activity, is used to treat rheumatoid arthritis and can cause endoplasmic reticulum (ER) stress by inhibiting sarco/ER Ca2 +-ATPase activity in cancer cells. This study aimed to investigate the correlation between celecoxib-induced ER stress and the effects of celecoxib against cell death signaling. Treatment of human colon cancer HCT116 cells with celecoxib reduced their viability and resulted in a loss of mitochondrial membrane potential ([Formula: see text]). Additionally, celecoxib treatment reduced the expression of genes involved in mitochondrial biogenesis and metabolism such as mitochondrial transcription factor A (TFAM) and uncoupling protein 2 (UCP2). Furthermore, celecoxib reduced transmembrane protein 117 (TMEM117), and RNAi-mediated knockdown of TMEM117 reduced TFAM and UCP2 expressions. These results suggest that celecoxib treatment results in the loss of [Formula: see text] by reducing TMEM117 expression and provide insights for the development of novel drugs through TMEM117 expression.

Temporal and Locational Values of Images Affecting the Deep Learning of Cancer Stem Cell Morphology.

Deep learning is being increasingly applied for obtaining digital microscopy image data of cells. Well-defined annotated cell images have contributed to the development of the technology. Cell morphology is an inherent characteristic of each cell type. Moreover, the morphology of a cell changes during its lifetime because of cellular activity. Artificial intelligence (AI) capable of recognizing a mouse-induced pluripotent stem (miPS) cell cultured in a medium containing Lewis lung cancer (LLC) cell culture-conditioned medium (cm), miPS-LLCcm cell, which is a cancer stem cell (CSC) derived from miPS cell, would be suitable for basic and applied science. This study aims to clarify the limitation of AI models constructed using different datasets and the versatility improvement of AI models. The trained AI was used to segment CSC in phase-contrast images using conditional generative adversarial networks (CGAN). The dataset included blank cell images that were used for training the AI but they did not affect the quality of predicting CSC in phase contrast images compared with the dataset without the blank cell images. AI models trained using images of 1-day culture could predict CSC in images of 2-day culture; however, the quality of the CSC prediction was reduced. Convolutional neural network (CNN) classification indicated that miPS-LLCcm cell image classification was done based on cultivation day. By using a dataset that included images of each cell culture day, the prediction of CSC remains to be improved. This is useful because cells do not change the characteristics of stem cells owing to stem cell marker expression, even if the cell morphology changes during culture.

Role of polyphenol in sugarcane molasses as a nutrient for hexavalent chromium bioremediation using bacteria.

Biological methods for the removal of hexavalent chromium (Cr(VI)) from contaminated sites are safe and efficient. This is especially true because they employ microorganisms and nutrients. The use of appropriate nutrients is important for the methods to be economically feasible. This paper aims to investigate the role of polyphenol from sugarcane molasses, an inexpensive material derived from the waste of the sugar industry, as a nutrient that efficiently provides carbon for Cr(VI)-removing bacteria. The colored constituents of sugarcane molasses were characterized based on the activity of Cr(VI)-reduction and the support of bacterial growth. Molasses promoted Cr(VI)-reducing activity in a pH dependent manner. The activity was related to the colored constituents, excluding sugar, by using absorbent-column chromatography. Moreover, the activity was closely related to the polyphenol fractions, which were slightly different from those of the colored constituents. Unlike the colored constituents, the isolated sugar was sufficient to support the growth of bacteria. Polyphenols from sugarcane molasses could reduce Cr(VI) with no effect on bacterial growth. The removal of Cr(VI) combining molasses and Cr(VI)-reducing bacteria may present an additive and/or synergistic effect.

FGF21 Alleviates Hepatic Endoplasmic Reticulum Stress under Physiological Conditions.

Fibroblast growth factor 21 (FGF21), mainly synthesized and secreted from the liver, is an endocrine FGF that regulates glucose and fatty acid metabolism to maintain whole body energy homeostasis. Gene expression of FGF21 was previously reported to be induced by endoplasmic reticulum (ER) stress through activating transcription factor 4 (ATF4). It has been reported that drug-induced ER stress is reduced by overexpression of FGF21. However, the function of endogenous FGF21 under physiological conditions such as the postprandial state remains unknown. Here, we examined the effects of both endogenous and exogenous FGF21 on postprandial hepatic ER stress. In mice, postprandial and tunicamycin-induced ER stress was significantly reduced by overexpression of FGF21 using a recombinant adenovirus. FGF21-deficient mice exhibited a more considerable increase in drug-induced ER stress target gene expression than wild-type mice. Following refeeding after fasting, FGF21 deficiency caused severe ER stress in the liver. The postprandial ER stress response was significantly reduced when hepatic FGF21 gene expression was increased by feeding a diet containing the soy protein ß-conglycinin which activates ATF4. Together, these results demonstrate that FGF21 reduces the increased expression of a subset of genes in the liver in response to ER stress and may correct metabolic disorders caused by ER stress.

Searching for novel ATF4 target genes in human hepatoma cells by microarray analysis.

Activating transcription factor 4 (ATF4) is a transcription factor with an important biological activity. ATF4 is induced by various stresses, such as endoplasmic reticulum stress, through the phosphorylation of eukaryotic translation initiation factor 2α. ATF4 is also involved in lipid metabolism. In the present study, we performed a microarray experiment to identify new ATF4 target genes, particularly those involved in lipid metabolism, and identified C12orf39, CSTA, and CALCB as novel ATF4 target genes. An amino acid response element (AARE) as an ATF4-binding site is present in the promoter regions of these genes. In a detailed analysis using luciferase assay, we showed that ATF4 activated C12orf39 promoter activity and that this activation was diminished by deletion or mutation of the AARE sequence in the promoter region. Our results suggest that C12orf39, CSTA, and CALCB are novel ATF4 target genes and that C12orf39 promoter activity is activated by ATF4 through AARE.

Fibroblast growth factor 21 induction by activating transcription factor 4 is regulated through three amino acid response elements in its promoter region.

Fibroblast growth factor 21 (FGF21) is an endocrine growth factor, a regulator of fatty acids and glucose metabolism. Recently, it has been reported that FGF21 expression is regulated by activating transcription factor 4 (ATF4), a transcription factor activated by various stimuli such as endoplasmic reticulum (ER) stress. ATF4 binds to the amino acid response element (AARE), a binding site for ATF4, in the promoter region of the target genes. The two response elements for ATF4 (AARE1 and AARE2) have been reported in the promoter region of FGF21 gene. In this study, we found a novel response element, located upstream of AARE1 and AARE2, essential for a promoter activation of FGF21. When this DNA sequence, named AARE3, was mutated, the promoter activation by ATF4 or ER stress was strongly decreased. Our results showed that the FGF21 promoter contains three response elements for ATF4, suggesting that FGF21 is a sensitive target of ATF4.

Selective Regulation of FGF19 and FGF21 Expression by Cellular and Nutritional Stress.

Fibroblast growth factor 19 (FGF19) and FGF21 are members of a subfamily of the FGFs called endocrine FGFs. FGF19 regulates the bile acid synthetic pathway. FGF19 expression is induced by farnesoid X receptor (FXR), a nuclear hormone receptor activated by bile acids in the small intestine. FGF21 plays an important role in lipolysis that occurs in white adipose tissue. FGF21 expression is stimulated by the nuclear fatty acid receptor peroxisome proliferator-activated receptor α (PPARα) in the liver. FGF19 and FGF21 were recently identified as targets of activating transcription factor 4 (ATF4), which is activated in response to endoplasmic reticulum (ER) stress. ATF4 is also activated by oxidative stress and amino acid deprivation. In this study, we investigated FGF19 and FGF21 expression in response to oxidative stress and amino acid deprivation. We found that FGF19 mRNA is induced by oxidative stress inducers in Caco-2 cells, which are derived from the human intestinal epithelium, and rat intestinal epithelial IEC6 cells. In contrast, ileal FGF15 expression, the rodent ortholog of human FGF19, is not increased by oxidative stress. No notable changes in expression of FGF15/19 took place under amino acid deprivation either in vitro or in vivo. In contrast, FGF21 expression is induced by oxidative stress and amino acid deprivation both in vitro and in vivo. These results indicate distinctive patterns of regulation of FGF19 expression by ER stress, and FGF21 expression by ER stress, oxidative stress, and amino acid deprivation through ATF4 activation.

ATF6α stimulates cholesterogenic gene expression and de novo cholesterol synthesis.

The activating transcription factor 6α (ATF6α) is a sensor of the endoplasmic reticulum stress response that regulates the expression of genes involved in the unfolded protein response. Here we found that forced expression of a constitutively active form of ATF6α, ATF6(N), stimulated the expression of cholesterogenic genes, including 3-hydroxy-3-methyl-glutaryl (HMG)-CoA reductase, HMG-CoA synthase, and squalene synthase, and de novo cholesterol synthesis in hepatoma Huh-7 cells. An ATF6α mutant lacking the DNA-binding domain ATF6(N)ΔbZip failed to show these effects. Luciferase assays indicated that ATF6(N) overexpression stimulated the promoter activities of HMG-CoA reductase, HMG-CoA synthase, and squalene synthase. Chromatin immunoprecipitation assays revealed that ATF6(N) interacted with the promoter region of the HMG-CoA synthase gene. Collectively, these results indicate that ATF6α can regulate de novo cholesterol synthesis through stimulation of cholesterogenic gene expression.

FGF19 (fibroblast growth factor 19) as a novel target gene for activating transcription factor 4 in response to endoplasmic reticulum stress.

FGF19 (fibroblast growth factor 19), expressed in the small intestine, acts as an enterohepatic hormone by mediating inhibitory effects on the bile acid synthetic pathway and regulating carbohydrate and lipid metabolism. In an attempt to identify novel agents other than bile acids that induce increased FGF19 expression, we found that some ER (endoplasmic reticulum) stress inducers were effective. When intestinal epithelial Caco-2 cells were incubated with thapsigargin, marked increases were observed in the mRNA and secreted protein levels of FGF19. This was not associated with the farnesoid X receptor. Reporter gene analyses using the 5'-promoter region of FGF19 revealed that a functional AARE (amino-acid-response element) was localized in this region, and this site was responsible for inducing its transcription through ATF4 (activating transcription factor 4), which is activated in response to ER stress. EMSAs (electrophoretic mobility-shift assays) and ChIP (chromatin immunoprecipitation) assays showed that ATF4 bound to this site and enhanced FGF19 expression. Overexpression of ATF4 in Caco-2 cells induced increased FGF19 mRNA expression, whereas shRNA (short hairpin RNA)-mediated depletion of ATF4 significantly attenuated a thapsigargin-induced increase in FGF19 mRNA.