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CDy1 is a powerful tool to distingusih embryonic stem cells for reprogramming studies and regeneration medicine. However, the stem cell selectivity mechanism of CDy1 has not been fully understood. Here, we report ALDH2 and ABCB1 as the molecular targets of CDy1, elucidated by live-cell affinity-matrix and ABC transporter CRISPRa library screening. The two unique orthogonal mechanisms provide the potential of multi-demensional cellular distinction of specific cell types., CDy1 is a powerful tool to distingusih embryonic stem cells for reprogramming studies and regeneration medicine.

The depside and depsidone series compounds of polyketide origin accumulate in the cortical or medullary layers of lichen thalli. Despite the taxonomic and ecological significance of lichen chemistry and its pharmaceutical potentials, there has been no single piece of genetic evidence linking biosynthetic genes to lichen substances. Thus, we systematically analyzed lichen polyketide synthases (PKSs) for categorization and identification of the biosynthetic gene cluster (BGC) involved in depside/depsidone production. Our in-depth analysis of the interspecies PKS diversity in the genus Cladonia and a related Antarctic lichen, Stereocaulon alpinum, identified 45 BGC families, linking lichen PKSs to 15 previously characterized PKSs in nonlichenized fungi. Among these, we identified highly syntenic BGCs found exclusively in lichens producing atranorin (a depside). Heterologous expression of the putative atranorin PKS gene (coined atr1) yielded 4-O-demethylbarbatic acid, found in many lichens as a precursor compound, indicating an intermolecular cross-linking activity of Atr1 for depside formation. Subsequent introductions of tailoring enzymes into the heterologous host yielded atranorin, one of the most common cortical substances of macrolichens. Phylogenetic analysis of fungal PKS revealed that the Atr1 is in a novel PKS clade that included two conserved lichen-specific PKS families likely involved in biosynthesis of depsides and depsidones. Here, we provide a comprehensive catalog of PKS families of the genus Cladonia and functionally characterize a biosynthetic gene cluster from lichens, establishing a cornerstone for studying the genetics and chemical evolution of diverse lichen substances. IMPORTANCE Lichens play significant roles in ecosystem function and comprise about 20% of all known fungi. Polyketide-derived natural products accumulate in the cortical and medullary layers of lichen thalli, some of which play key roles in protection from biotic and abiotic stresses (e.g., herbivore attacks and UV irradiation). To date, however, no single lichen product has been linked to respective biosynthetic genes with genetic evidence. Here, we identified a gene cluster family responsible for biosynthesis of atranorin, a cortical substance found in diverse lichen species, by categorizing lichen polyketide synthase and reconstructing the atranorin biosynthetic pathway in a heterologous host. This study will help elucidate lichen secondary metabolism, harnessing the lichen's chemical diversity, hitherto obscured due to limited genetic information on lichens.

Mucosal-associated invariant T (MAIT) cells exhibit different characteristics from those of TCRα7.2− conventional T cells. They play important roles in various inflammatory diseases, including rheumatoid arthritis and inflammatory bowel disease. MAIT cells express a single T cell receptor alpha chain, TCRα7.2 segment associated with Jα33 and CDR3 with fixed length, which recognizes bacteria-derived vitamin B metabolites. However, the characteristics of MAIT cells and TCRα7.2+ CD161− T cells have never been compared. Here, we performed RNA sequencing to compare the properties of MAIT cells, TCRα7.2− conventional T cells and TCRα7.2+ CD161− T cells. Genome-wide transcriptomes of MAIT cells, TCRα7.2− conventional T cells, and TCRα7.2+ CD161− T cells were compared and analyzed using causal network analysis. This is the first report comparing the transcriptomes of MAIT cells, TCRα7.2− conventional T cells and TCRα7.2+ CD161− T cells. We also identified the predominant signaling pathways of MAIT cells, which differed from those of TCRα7.2− conventional T cells and TCRα7.2+ CD161− T cells, through a gene set enrichment test and upstream regulator analysis and identified the genes responsible for the characteristic MAIT cell phenotypes. Our study advances the complete understanding of MAIT biology.

Background Distant metastasis is the major cause of death in patients with colorectal cancer (CRC). Previously, we identified KITENIN as a metastasis-enhancing gene and suggested that the oncogenic KITENIN complex is involved in metastatic dissemination of KITENIN-overexpressing CRC cells. Here, we attempted to find substances targeting the KITENIN complex and test their ability to suppress distant metastasis of CRC. Methods We screened a small-molecule compound library to find candidate substances suppressing the KITENIN complex in CRC cells. We selected a candidate compound and examined its effects on the KITENIN complex and distant metastasis through in vitro assays, a molecular docking model, and in vivo tumor models. Results Among several compounds, we identified DKC1125 (Disintegrator of KITENIN Complex #1125) as the best candidate. DKC1125 specifically suppressed KITENIN gain of function. After binding KH-type splicing regulatory protein (KSRP), DKC1125 degraded KITENIN and Dvl2 by recruiting RACK1 and miRNA-124, leading to the disintegration of the functional KITENIN–KSRP–RACK1–Dvl2 complex. A computer docking model suggested that DKC1125 specifically interacted with the binding pocket of the fourth KH-domain of KSRP. KITENIN-overexpressing CRC cells deregulated certain microRNAs and were resistant to 5-fluorouracil, oxaliplatin, and cetuximab. DKC1125 restored sensitivity to these drugs by normalizing expression of the deregulated microRNAs, including miRNA-124. DKC1125 effectively suppressed colorectal liver metastasis in a mouse model. Interestingly, the combination of DKC1125 with 5-fluorouracil suppressed metastasis more effectively than either drug alone. Conclusion DKC1125 targets the KITENIN complex and could therefore be used as a novel therapeutic to suppress liver metastasis in CRC expressing high levels of KITENIN.

Usnic acid (UA), a lichen secondary substance, has considerable anticancer activity in vitro, whereas its effect in vivo is limited. Here, potassium usnate (KU) was prepared by the salinization of UA to enhance its water solubility. KU showed increased bioavailability compared with UA in the tumor, liver, and plasma of a CT26 syngeneic mouse tumor xenograft model after oral administration, as determined by LC-MS/MS analysis. KU exhibited potent anticancer effects on colorectal cancer cells and inhibited liver metastasis in an orthotopic murine colorectal cancer model. KU treatment downregulated the epithelial-mesenchymal markers Twist, Snail, and Slug and the metastasis-related genes CAPN1, CDC42, CFL1, IGF1, WASF1, and WASL in cells and tumor tissues. The present results suggest the potential application of the water-soluble form of UA, KU, in anticancer therapy.

Tumor initiating cells (TIC) are resistant to conventional anticancer therapy and associated with metastasis and relapse in cancer. Although various TIC markers and their antibodies have been proposed, it is limited to the use of antibodies for in vivo imaging or treatment of TIC. In this study, we discovered heme oxygenase 2 (HMOX2) as a novel biomarker for TIC and developed a selective small molecule probe TiNIR (tumor initiating cell probe with near infrared). TiNIR detects and enriches the functionally active TIC in human lung tumors, and through the photoacoustic property, TiNIR also visualizes lung TIC in the patient-derived xenograft (PDX) model. Furthermore, we demonstrate that TiNIR inhibits tumor growth by blocking the function of HMOX2, resulting in significantly increased survival rates of the cancer model mice. The novel therapeutic target HMOX2 and its fluorescent ligand TiNIR will open a new path for the molecular level of lung TIC diagnosis and treatment.

Lichens produce various unique chemicals that are used in the pharmaceutical industry. To screen for novel lichen secondary metabolites that inhibit the stemness potential of colorectal cancer cells, we tested acetone extracts of 11 lichen samples collected in Chile. Tumidulin, isolated from Niebla sp., reduced spheroid formation in CSC221, DLD1, and HT29 cells. In addition, mRNA expressions and protein levels of cancer stem markers aldehyde dehydrogenase-1 (ALDH1), cluster of differentiation 133 (CD133), CD44, Lgr5, and Musashi-1 were reduced after tumidulin treatment. Tumidulin decreased the transcriptional activity of the glioma-associated oncogene homolog zinc finger protein (Gli) promoter in reporter assays, and western blotting confirmed decreased Gli1, Gli2, and Smoothened (SMO) protein levels. Moreover, the tumidulin activity was not observed in the presence of Gli and SMO inhibitors. Together, these results demonstrate for the first time that tumidulin is a potent inhibitor of colorectal cancer cell stemness.

In endothermic species, heat released as a product of metabolism ensures stable internal temperature throughout the organism, despite varying environmental conditions. Mitochondria are major actors in this thermogenic process. Part of the energy released by the oxidation of respiratory substrates drives ATP synthesis and metabolite transport, but a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured mitochondrial temperature in situ under different physiological conditions. At a constant external temperature of 38 °C, mitochondria were more than 10 °C warmer when the respiratory chain (RC) was fully functional, both in human embryonic kidney (HEK) 293 cells and primary skin fibroblasts. This differential was abolished in cells depleted of mitochondrial DNA or treated with respiratory inhibitors but preserved or enhanced by expressing thermogenic enzymes, such as the alternative oxidase or the uncoupling protein 1. The activity of various RC enzymes was maximal at or slightly above 50 °C. In view of their potential consequences, these observations need to be further validated and explored by independent methods. Our study prompts a critical re-examination of the literature on mitochondria., Author summary To ensure a stable internal temperature, endothermic species make use of the heat released during the final steps of food burning by the mitochondria present in all cells of the organism. Indeed, only a fraction of the energy released by the oxidation of respiratory substrates is used to generate ATP, while a substantial proportion is released as heat. Using a temperature-sensitive fluorescent probe targeted to mitochondria, we measured the temperature of active mitochondria in cultured intact human cells. Mitochondria were found to be more than 10 °C warmer when the respiratory chain was functional. This differential was abolished in cells depleted of mitochondrial DNA or by respiratory inhibitors but preserved or enhanced by the expression of thermogenic enzymes such as Ciona alternative oxidase or by uncoupling protein 1. The activity of various respiratory chain enzymes was found to be maximal near 50 °C. Note that in view of their potential consequences, the observations reported here need to be validated and explored further by independent methods.

Summary Glycolytic enzymes are attractive anticancer targets. They also carry out numerous, nonglycolytic "moonlighting" functions in cells. In this study, we investigated the anticancer activity of the triazine small molecule, GAPDS, that targets the glycolytic enzyme glyceraldehyde 3-phosphate dehydrogenase (GAPDH). GAPDS showed greater toxicity against cancer cells compared to a known GAPDH enzyme inhibitor. GAPDS also selectively inhibited cell migration and invasion. Our analysis showed that GAPDS treatment reduced GAPDH levels in the cytoplasm, which would modulate the secondary, moonlighting functions of this enzyme. We then used GAPDS as a probe to demonstrate that a moonlighting function of GAPDH is tubulin regulation, which may explain its anti-invasive properties. We also observed that GAPDS has potent anticancer activity in vivo. Our study indicates that strategies to target the secondary functions of anticancer candidates may yield potent therapeutics and useful chemical probes.

Background Myeloid-derived suppressor cells (MDSCs) are immature myeloid cells with inhibitory effects on T cell proliferation. MDSC are over-amplified in most cancer patients so that cancer cells avoid anticancer immunity. Unlike mouse MDSCs, however, specific surface markers to define human MDSCs is still controversial due its complexity of subsets. Heptamethine cyanine dyes are fluorescent dyes, particularly used for noninvasive in vivo imaging and detection of cancer. MHI-148 is known to be specifically retained by tumor cells but not by normal cells. In this study, we investigated the potential application of MHI-148 as a specific MDSC detection probe. Methods Mice bearing 4T1 breast cancer cells were created in female BALB/c mice. Splenocytes were isolated at 21 days after injection. Cells were stained with anti-Gr-1-FITC, anti-CD11b-PE antibodies for MDSCs or with MHI-148 dye followed by isolating positive cells with cell sorter. To determine whether MHI148-positive cells possess inhibitory effect on T-cell proliferation, EdU-based T cell proliferation assay was performed. Arginase assay and measurement of Nitrite production were also performed for assessing T cell activity inhibition. Results Compared to normal mice, tumor-bearing mice showed tremendous increase of MDSCs (CD11b+/Gr-1+). Over 81% of these MDSCs in tumor bearing mice were reactive to MHI-148 dye. Most sorted cell for MHI-148 fluorescence was also CD11b+/Gr-1+ MDSCs (97.7 %). Notably, lymphocytes and monocytes were not reactive to MHI-148. In addition, MHI-148 dye-positive cells significantly reduced T cell proliferation with increased arginase activity and nitrites concentration, suggesting that MHI-148 reacts to the cells possessing similar function of MDSCs. Conclusions This study demonstrates that MHI-148 reacts to mouse CD11b+/Gr-1+ PBMCs with the function of MDSC characteristics. Further studies have be focused on MHI148 affinity to human MDSC and outcome of which will result in a novel tool to detect MDSC to be utilized to predict cancer patient prognosis. Legal entity responsible for the study The authors. Funding Has not received any funding. Disclosure All authors have declared no conflicts of interest.

Enolase is a component of the glycolysis pathway and a "moonlighting" protein, with important roles in diverse cellular processes that are not related to its function in glycolysis. However, small molecule tools to probe enolase function have been restricted to crystallography or enzymology. In this study, we report the discovery of the small molecule "ENOblock", which is the first, nonsubstrate analogue that directly binds to enolase and inhibits its activity. ENOblock was isolated by small molecule screening in a cancer cell assay to detect cytotoxic agents that function in hypoxic conditions, which has previously been shown to induce drug resistance. Further analysis revealed that ENOblock can inhibit cancer cell metastasis in vivo. Moreover, an unexpected role for enolase in glucose homeostasis was revealed by in vivo analysis. Thus, ENOblock is the first reported enolase inhibitor that is suitable for biological assays. This new chemical tool may also be suitable for further study as a cancer and diabetes drug candidate.

Fluorescence labelling of an intracellular biomolecule in native living cells is a powerful strategy to achieve in-depth understanding of the biomolecule's roles and functions. Besides being nontoxic and specific, desirable labelling probes should be highly cell permeable without nonspecific interactions with other cellular components to warrant high signal-to-noise ratio. While it is critical, rational design for such probes is tricky. Here we report the first predictive model for cell permeable background-free probe development through optimized lipophilicity, water solubility and charged van der Waals surface area. The model was developed by utilizing high-throughput screening in combination with cheminformatics. We demonstrate its reliability by developing CO-1 and AzG-1, a cyclooctyne- and azide-containing BODIPY probe, respectively, which specifically label intracellular target organelles and engineered proteins with minimum background. The results provide an efficient strategy for development of background-free probes, referred to as ‘tame' probes, and novel tools for live cell intracellular imaging., The success of a fluorescent dye as a molecular probe to monitor the intracellular activity of biomolecules depends on its physicochemical characteristics. Here, the authors use a predictive model to identify key features that allow them to design cell permeable, background-free fluorescent probes.

Current strategies to monitor reprogramming into induced pluripotent stem cells (iPSCs) are limited in that they rely on the recognition of advanced stage biomarkers or they involve the transduction of genetically-modified cells. These limitations are particularly problematic in high-throughput screenings where cell availability, low cost and a rapid experimental protocol are critical issues. Herein we report the application of a pluripotent stem cell fluorescent probe (i.e. CDy1) as a reporter for the rapid screening of chemicals in reprogramming iPSCs. CDy1 stains early-stage iPSCs at 7dpi as well as matured iPSCs; hence it can partially overcome the slow kinetics of the reprogramming process. As a proof of concept, we employed a CDy1-based screening in 384 well-plates to examine the effect of newly synthesized hydroxamic acid derivatives in reprogramming mouse fibroblasts transduced with Oct4, Sox2 and Klf-4 without c-Myc. One compound (1–26) was identified as a reprogramming enhancer by 2.5-fold and we confirmed that 1–26 behaves as a histone deacetylase (HDAC) inhibitor. The successful identification of novel small molecules enhancing the generation of iPSCs by means of a rapid and simple protocol demonstrates the suitability of this CDy1-based screening platform for the large scale and high-throughput evaluation of iPSC modulators.

Detecting and isolating specific types of cells is crucial to understanding a variety of biological processes, including development, aging, regeneration and pathogenesis; this understanding, in turn, allows the use of cells for therapeutic purposes, for which stem cells have emerged recently as invaluable materials. The current methods of isolation and characterization of stem cells depend on cell morphology in culture or on immunostaining of specific markers. These methods are, however, time consuming and involve the use of antibodies that may often make the cells unsuitable for further study. We recently developed a fluorescent small molecule named CDy1 (compound of designation yellow 1) that selectively stains live embryonic stem cells (ESCs) and induced pluripotent stem cells (iPSCs). This protocol describes detailed procedures for staining ESC and iPSC in live conditions and for fluorescence-activated cell sorting (FACS) of ESC using CDy1. Cell staining, image acquisition and FACS can be done within 6 h.

Alzheimer's disease is the major cause of senile dementia with the hallmark of beta-amyloid deposition in neurons. Although the main cause(s) of this deposition is not fully understood, however, the wealth of the present literature data supports the pivotal role of reactive oxygen and nitrogen species in both the initiation and progression of beta-amyloid aggregation and deposition. In the present study, we were interested to evaluate the free-radical protecting effect of AA3E2, a triazine derivative with a beta-amyloid-breaking activity, among SK-N-MC neuroblastoma cells exposed to hydrogen peroxide (H(2)O(2)) as an exogenous source of free radicals. Exposure of the cells to different doses of AA3E2 (1-16 microM) for 3h followed by subsequent exposure to a single dose of H(2)O(2) (mainly 150 microM) attenuated the extent of superoxide dismutase (SOD) and catalase (CAT) inhibition by H(2)O(2), in a dose dependent manner. Furthermore, significant reduction was observed in the extent of cellular lactate dehydrogenase release, intracellular ROS and the extent of apoptosis among the cells pre-treated with AA3E2. Based on these data, an antioxidant mode of action is proposed for AA3E2 besides its previously beta-amyloid-breaking activity.

Genetic and biochemical studies suggest that Alzheimer's disease (AD) is caused by a series of events initiated by the production and subsequent aggregation of the Alzheimer's amyloid beta peptide (Abeta), the so-called amyloid cascade hypothesis. Thus, a logical approach to treating AD is the development of small molecule inhibitors that either block the proteases that generate Abeta from its precursor (beta- and gamma-secretases) or interrupt and/or reverse Abeta aggregation. To identify potent inhibitors of Abeta aggregation, we have developed a high-throughput screen based on an earlier selection that effectively paired the folding quality control feature of the Escherichia coli Tat protein export system with aggregation of the 42-residue AD pathogenesis effecter Abeta42. Specifically, a tripartite fusion between the Tat-dependent export signal ssTorA, the Abeta42 peptide and the beta-lactamase (Bla) reporter enzyme was found to be export incompetent due to aggregation of the Abeta42 moiety. Here, we reasoned that small, cell-permeable molecules that inhibited Abeta42 aggregation would render the ssTorA-Abeta42-Bla chimera competent for Tat export to the periplasm where Bla is active against beta-lactam antibiotics such as ampicillin. Using a fluorescence-based version of our assay, we screened a library of triazine derivatives and isolated four nontoxic, cell-permeable compounds that promoted efficient Tat-dependent export of ssTorA-Abeta42-Bla. Each of these was subsequently shown to be a bona fide inhibitor of Abeta42 aggregation using a standard thioflavin T fibrillization assay, thereby highlighting the utility of our bacterial assay as a useful screen for antiaggregation factors under physiological conditions.

Novel heterocyclic ring-substituted pyrimidines have been designed as inhibitors of glycogen synthase kinase-3beta (GSK-3beta) from the modification of known inhibitors. Several potent inhibitors exhibiting nanomolar activities were discovered against GSK-3beta kinase as well as in an NF-kappaB reporter gene assay. Based on the results from in vitro TNF-alpha release inhibition and in vivo endotoxima, these inhibitors are expected to be useful candidates for treatment of inflammation-related diseases.

Lichens are symbiotic organisms that produce various unique chemicals that can be used for pharmaceutical purposes. With the aim of screening new anti-cancer agents that inhibit cancer cell motility, we tested the inhibitory activity of seven lichen species collected from the Romanian Carpathian Mountains against migration and invasion of human lung cancer cells and further investigated the molecular mechanisms underlying their anti-metastatic activity. Among them, Alectoria samentosa, Flavocetraria nivalis, Alectoria ochroleuca, and Usnea florida showed significant inhibitory activity against motility of human lung cancer cells. HPLC results showed that usnic acid is the main compound in these lichens, and (+)-usnic acid showed similar inhibitory activity that crude extract have. Mechanistically, beta-catenin-mediated TOPFLASH activity and KITENIN-mediated AP-1 activity were decreased by (+)-usnic acid treatment in a dose-dependent manner. The quantitative real-time PCR data showed that (+)-usnic acid decreased the mRNA level of CD44, Cyclin D1 and c-myc, which are the downstream target genes of both beta-catenin/LEF and c-jun/AP-1. Also, Rac1 and RhoA activities were decreased by treatment with (+)-usnic acid. Interestingly, higher inhibitory activity for cell invasion was observed when cells were treated with (+)-usnic acid and cetuximab. These results implied that (+)-usnic acid might have potential activity in inhibition of cancer cell metastasis, and (+)-usnic acid could be used for anti-cancer therapy with a distinct mechanisms of action.

Lichens produce various unique chemicals that can be used for pharmaceutical purposes. To screen for novel lichen secondary metabolites showing inhibitory activity against lung cancer cell motility, we tested acetone extracts of 13 lichen samples collected in Chile. Physciosporin, isolated from Pseudocyphellaria coriacea (Hook f. & Taylor) D.J. Galloway & P. James, was identified as an effective compound and showed significant inhibitory activity in migration and invasion assays against human lung cancer cells. Physciosporin treatment reduced both protein and mRNA levels of N-cadherin with concomitant decreases in the levels of epithelial-mesenchymal transition markers such as snail and twist. Physciosporin also suppressed KITENIN (KAI1 C-terminal interacting tetraspanin)-mediated AP-1 activity in both the absence and presence of epidermal growth factor stimulation. Quantitative real-time PCR analysis showed that the expression of the metastasis suppressor gene, KAI1, was increased while that of the metastasis enhancer gene, KITENIN, was dramatically decreased by physciosporin. Particularly, the activity of 3'-untranslated region of KITENIN was decreased by physciosporin. Moreover, Cdc42 and Rac1 activities were decreased by physciosporin. These results demonstrated that the lichen secondary metabolite, physciosporin, inhibits lung cancer cell motility through novel mechanisms of action.

Purpose: Understanding the complex biological functions of E3-ubiquitin ligases may facilitate the modulation of E3-ubiquitin ligases as a promising approach for the development of novel anticancer drugs. We recently identified that the KITENIN/ErbB4-Dvl2-c-Jun axis works as a novel unconventional downstream signal of epidermal growth factor in colorectal cancer (CRC) tissues and that the immunohistochemical expression of KITENIN/ErbB4 was highly expressed in tumor tissues from advanced CRC stage. However, the detailed mechanisms that explain the higher levels of ErbB4 in colon cancer tissues are largely unknown. Here we investigated whether E3-ubiquitin ligases participate in the operation of the KITENIN/ErbB4-Dvl2-c-Jun axis and in the maintenance of elevated KITENIN/ErbB4 complex in CRC. Results & Discussion: We found that Nrdp1, an E3-ligase for ErbB3/ErbB4, interacted with KITENIN (KAI1 C-terminal interacting tetraspanin) to form a functional KITENIN/ErbB4/Nrdp1 complex and is responsible for down-regulating Dvl2 within this complex. Interestingly, ErbB4 was resistant to degradation by Nrdp1 in KITENIN/Nrdp1-co-transfected CRC cells, and KITENIN bound to the C-terminal coiled-coil domain of Nrdp1. Chemical blockade of ErbB kinase did not block the action of EGF to increase in total/phospho-ErbB4 and phospho-ERK in KITENIN/ErbB4-cotransfected cells, whereas it blocked the action of EGF in ErbB4 alone-transfected CRC cells. In human CRC tissues, higher expressions of ErbB4 and KITENIN and lower expression of Dvl2 was observed in stage IV samples than in stage I, but a low level of Nrdp1 was expressed in both stages and it did not differ significantly by stage. These results indicated that Nrdp1 is necessary for the reduction in Dvl2 to generate c-Jun in the EGF-KITENIN/ErbB4-c-Jun axis, but more importantly, elevated KITENIN protects KITENIN-bound ErbB4 from Nrdp1-mediated degradation via physical collaboration between the KITENIN/ErbB4 complex and Nrdp1, but not via modulation of ErbB kinase activity. Thus, KITENIN functions in the maintenance of a higher expression level of ErbB4 in advanced CRC tissues, independent of ubiquitin-mediated degradation via Nrdp1. Conclusion: Our present findings add a new component to our understanding of the molecular events underlying the regulation of ErbB4 expression level in CRC tissues: KITENIN is also a fine regulator of ErbB4 expression in addition to E3-ubiquitin ligase Nrdp1. Citation Format: Jeong A Bae, Eun Gene Sun, Yoo-Seung Ko, Hui Jeong Choi, Chaeyong Jung, Kyung-Hwa Lee, Ik Joo Chung, Kyung-Sub Moon, Young Hyun Yu, Hyung-Ho Ha, Hangun Kim, Kyung Keun Kim. KITENIN works as a fine regulator of ErbB4 expression in colorectal cancer tissues in addition to E3-ubiquitin ligase Nrdp1 [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2017; 2017 Apr 1-5; Washington, DC. Philadelphia (PA): AACR; Cancer Res 2017;77(13 Suppl):Abstract nr 3530. doi:10.1158/1538-7445.AM2017-3530

Abnormal tau aggregates are presumed to be neurotoxic and are an important therapeutic target for multiple neurodegenerative disorders including Alzheimer’s disease. Growing evidence has shown that tau intermolecular disulfide cross-linking is critical in generating tau oligomers that serve as a building block for higher-order aggregates. Here we report that a small molecule inhibitor prevents tau aggregation by blocking the generation of disulfide cross-linked tau oligomers. Among the compounds tested, a rosamine derivative bearing mild thiol reactivity selectively labeled tau and effectively inhibited oligomerization and fibrillization processes in vitro. Our data suggest that controlling tau oxidation status could be a new therapeutic strategy for prevention of abnormal tau aggregation.

A better understanding of the cellular and molecular mechanisms involved in the reprogramming of somatic cells is essential for further improvement of induced pluripotent stem (iPS) cell technology. In this study, we enriched for cells actively undergoing reprogramming at different time points by sorting the cells stained with a stem cell-selective fluorescent chemical probe CDy1 for their global gene expression analysis. Day-to-day comparison of differentially expressed genes showed highly dynamic and transient gene expressions during reprogramming, which were largely distinct from those of fully-reprogrammed cells. An unbiased analysis of functional regulation indicated robust modulation of concurrent programs at critical junctures. Globally, transcriptional programs involved in cell proliferation, morphology and signal transduction were instantly triggered as early as 3days-post-infection to prepare the cell for reprogramming but became somewhat muted in the final iPS cells. On the other hand, the highly coordinated metabolic reprogramming process was more gradually activated. Subsequent network analysis of differentially expressed genes indicated PDGF-BB as a core player in reprogramming which was verified by our gain- and loss-of-function experiments. As such, our study has revealed previously-unknown insights into the mechanisms of cellular reprogramming.

Purpose: The molecular events in the malignant progression of colon adenoma after loss of adenomatous polyposis coli (APC) are not fully understood. KITENIN (KAI1 C-terminal interacting tetraspanin) increases the invasiveness of colorectal cancer (CRC) cells and we recently identified a novel EGFR-independent oncogenic signal of EGF that works under co-expressed KITENIN and ErbB4. Here we tested whether elevated KITENIN and ErbB4 contributes to further progression of intestinal adenoma following APC loss. Results & Discussion: The intestinal tissues of villin-KITENIN transgenic mice in which villin-driven elevated KITENIN induced increased c-Jun expression exhibit mild epithelial cell proliferation but no epithelial lineage changes, compared with those of non-transgenic mice. Among the 4 ErbB4 isoforms, JM-a/CYT-2 and JM-b/CYT-2 exhibited the highest AP-1 activity when cells co-expressing KITENIN and each isoform were stimulated by EGF. Interestingly, predominant overexpression of ErbB4 CYT-2 isoform mRNA as well as increased EGFR expression were observed in intestinal adenoma of APCmin/+ mice making the microenvironment of activated EGF signaling. When we crossed villin-KITENIN mice with APCmin/+ mice, intestinal tumor tissues in the crossed mice showed the characteristics of early stage invading adenocarcinoma. In CRC patients, ErbB4-CYT-2 mRNA expression was significantly greater in tumor tissues than in normal adjacent tissues, but no differences in tumoral expression between the stages, and a positive correlation exists between KITENIN and ErbB4-CYT-2 mRNA expression. Thus, elevated expression of KITENIN and ErbB4-CYT-2 is newly identified as a factor that promotes the transition of colon adenoma to adenocarcinoma within an APC-loss-associated tumor microenvironment. Conclusion: Higher mRNA expression of both KITENIN and ErbB4-CYT-2 in colon adenoma tissues can be used as a molecular marker of the possible development of malignant transformation. Citation Format: Jeong A Bae, Eun Gene Sun, Yoo-Seung Ko, Hui Jeong Choi, Woo-Kyun Bae, Sang-Hee Cho, Ik Joo Chung, Kyung-Sub Moon, Young-Hyun Yu, Hyung-Ho Ha, Hangun Kim, Kyung Keun Kim. Identification of higher mRNA expression of both Kitenin and ErbB4 CYT-2 isoform as a molecular marker for the prediction of transition from colon adenoma to carcinoma. [abstract]. In: Proceedings of the 107th Annual Meeting of the American Association for Cancer Research; 2016 Apr 16-20; New Orleans, LA. Philadelphia (PA): AACR; Cancer Res 2016;76(14 Suppl):Abstract nr 5150.

Fluorescent small-molecules become extensively used for live-cell imaging, but mainly in the context of labeling conjugates for other protein-binding motifs, such as antibodies.[1] As most fluorescent molecules are flat and hydrophobic, it has generally been believed that these fluorophores may bind to many hydrophobic proteins in cells, without any specificity.[2] This conventional wisdom, however, has not been tested systemically due to the lack of sufficiently diverse dye sources. Recently, we developed a diversity-oriented fluorescence library approach (DOFLA) to use fluorescent dyes to distinguish directly cellular components such as GTP,[3] DNA,[4] RNA,[5] heparin,[6] and organelles.[7] In this system, the diverse structural motifs of each dye molecule in the library endowed target selectivity. From these results, we envisioned that sufficient structural modifications of fluorophore scaffold could lead us to develop probes that label specific proteins from whole proteomes.[8] In addition to our recent finding of a fluorescein derivative labeling glutathione s-transferase,[9] here we report a rosamine derivative that labels tubulin in vitro and a mitochondrial protein in live cells. Previously a fluorescent small molecule capable of detecting differentiated myotubes was discovered from mitochondria-targeted rosamine library.[10, 11, 12] The hallmark of muscle differentiation is the fusion of mono-nucleated myoblasts to multi-nucleated myotubes.[13] During murine C2C12 myogenesis, the fluorescence intensity of one rosamine compound, E26, increased significantly. This myotube selectivity may be achieved by binding to one of the differentiation markers expressed more highly in myotubes; alternatively, the probe may detect other physiological changes after differentiation. When subjected for the further investigation, unfortunately, E26 showed photo-instability under strong and continuous light irradiation (Supplementary Fig. 1 online). The rosamine library compounds were retested under long-term light exposure and we selected two compounds (I25 and I31; Fig. 1) based on high photo-stability and fluorescence response after differentiation (I25: 2.4 ± 0.2, I31: 3.0 ± 0.5 fold increase, N = 3; Supplementary Fig. 2 online). Figure 1 Probes for myogenic differentiation In order to identify protein binders of these compounds, affinity matrices were prepared based on careful SAR studies (Fig. 2a). Affinity pull-down assay is the most conventional method for identification of small-molecule binding proteins.[14] Affinity resins were incubated with myotube lysates and washed with buffer to get rid of non-specific binders. Then, resin-bound proteins were separated by SDS-PAGE and stained with Coomassie blue (Fig. 2b). One enriched protein band at approximately 54 kDa was observed along with several other bands. To determine the specificity of protein binders to these compounds, competition assay was followed. Myotube cell lysate was pre-incubated with 100 µM of I25, I31, rhodamine 123, or rhodamine B before affinity pull-down. Figure 2 Identification of protein-binders in vitro vs. in living cells The strongest band at 54 kDa completely disappeared upon competition with unmodified I25 or I31, but not with rhodamine 123 or rhodamine B, which were included as structurally similar controls. Thus, we concluded that the 54 kDa band was the most convincing binding target protein of the compounds. The band was excised, sequenced, and identified to be tubulin (Supplementary Note 1 online). While affinity pull-down assay identified the major binder to be tubulin, a well-known cytosolic protein, our compounds appeared to be localized to mitochondria in live cells. Affinity-based isolation greatly depends on protein abundace as well as protein binding affinity. Since tubulin is a highly abundant protein in cells (10 ~ 20 µM),[15] despite the intrinsic affinity, its isolation might be an artifact. Therefore, we further explored the endogenus binding protein in the context of live cells. For live-cell investigation, we synthesized a cell-permeable chemical affinity derivative, which has a thiol reactive chloroacetyl group, to enable covalent binding to target proteins (Fig. 2c). The compound is named as CDy2, Compound of Designation yellow 2, following the biological convention of Cluster of Designation (CD) for cell-surface markers. The benefit of the chemical affinity probe is that once it forms a covalent bond with its targets in live cells. Those labeled proteins can be visualized by scanning the SDS-PAGE gel with a fluorescence scanner, even though the proteins are denatured. When applied to myoblasts and myotubes, CDy2 showed a 2.3-fold increase in fluorescence intensity after differentiation (2.3 ± 0.4 fold increase, N = 3; Fig. 2d), which is comparable to the increases observed with I25 and I31. To unveil the endogenus binding protein(s), myoblasts or myotubes were incubated with CDy2 for 1 hour. Labeled lysates were separated by SDS-PAGE and analyzed with a fluorescence scanner (Fig. 2d). Again, a unique fluorescently labeled band was observed around 54 kDa (Fig. 2e). Also, pre-treatment of myotubes with I31 reduced the intensity of CDy2-labeled protein band, indicating effective competition of CDy2 with I31 in live cells (Supplementary Fig. 3b online). To determine the identity of the labeled protein, cell lysates were separated by 2D-gel electrophoresis, and fluorescently labeled spots around 54 kDa were excised and sequenced (Fig. 2f; Supplementary Note 2 online). To our surprise, the major spots were found to be mitochondrial aldehyde dehydrogenase (ALDH2), not tubulin. To validate the binding in live cells, firstly ALDH2 or tubulin was overexpressed in HEK cells. Each protein was tagged with green fluorescent protein (GFP) to distinguish those from the endogenous proteins. Forty-eight hours after transfection, cells were labeled with CDy2 and each lysate was subjected to SDS-PAGE analysis (Fig. 3a); the HEK293 cell line was chosen because of its relatively high transfection efficiency. The result shows that CDy2 labeled ALDH2-GFP, but not tubulin-GFP. Secondly, ALDH2 expression was suppressed by siRNA (Fig. 3b). Upon ALDH2 knock-down, the CDy2-labeled band (54 kDa) was dramatically reduced. These siRNA and overexpression experiments clearly indicate that CDy2 selectively binds to ALDH2 in living cells. However, when treated to cell lysates, CDy2 labeled tubulin instead of ALDH2 (Supplementary Fig. 4d online). Altogether, these results suggest that CDy2 binds to two distinct proteins depending on the experimental environment. Figure 3 Validation of labeled protein identity in living cells In-gel fluorescence analysis showed that CDy2 labels ALDH2 stronger in myotubes over myoblast (Fig. 2e). Interestingly, however, the total amount of ALDH2 remained unchanged before and after differentiation. Thus it was necessary to determine the mechanism of CDy2 selectivity for myotubes. For example, the mitochondrial membrane potential of skeletal muscle is quite high, possibly due to increased energy requirements for muscle contractions;[13] this elevated membrane potential may cause the myotube-selectivity of CDy2. In fact, when cells were fixed with formaldehyde, CDy2 lost its mitochondrial preference, as well as its selectivity for myotubes (Supplementary Fig. 4a online). Further, the mitochondrial membrane potential was disrupted by treating cells with the mitochondrial uncoupler CCCP (carbonyl cyanide 3-chlorophenylhydrazone).[16] Upon pre-treatment with CCCP, the amount of fluorescently labeled protein was significantly reduced (Supplementary Fig. 4c online). These results support the notion that an increase in the mitochondrial membrane potential as a result of myogenesis gives rise to the selectivity of CDy2 for myotubes. Rosamine compounds are derivatives of rhodamine, which have long been used as mitochondrial probes. Their aromatic and cationic properties direct them to mitochondria due to the membrane potential across its bilayer.[17] The rosamine probes are sensitive to the incresed membrane potential after myogenic differentiation. Once localized in mitochondria, they labeled ALDH2 selectively. Although ALDH2 itself is not a differentiation marker, the selectivity to rosamine probes deserves careful consideration. Up until now, it has been generally believed that rhodamine dyes stain the mitochondrial membrane without showing specific interactions with mitochondrial proteins.[18] A cell is a highly ordered structure,[19] where small-molecule localization is precisely controlled based on chemical properties. Once a small molecule is sequestered in an organelle such as mitochondria, its interaction with proteins will be greatly limited within the cellular compartment. In this study, CDy2 showed an apparent binding affinity to tubulin in vitro, but resulted in binding to ALDH2 in live cells. This implies that CDy2 molecules are sequestered in mitochondria rapidly before they have a chance to react with tubulin in the cytoplasm. Elucidating small molecule’s binding protein is the most challenging part of chemical genetics work. Our observations cast important warning that the binding partner should be carefully evaluated in the context of the environmental factors.

There is an urgent need to discover new compounds that effectively treat diabetes by mimicking the action of insulin (insulin mimetics). Traditional approaches to studying anti-diabetic agents in cells are inconvenient for screening chemical libraries to identify insulin mimetics. 2-(N-(7-Nitrobenz-2-oxa-1,3-diazol-4-yl)amino)-2-deoxyglucose (2-NBDG) and 6-NBDG are fluorescent analogues of glucose that could be employed in screening. However, there are no published data about the use of these analogues to identify new insulin mimetics. We have developed a screening system based on 6-NBDG using 3T3-L1 adipocytes in a 96-well culture plate format. 6-NBDG was found to produce a larger signal than 2-NBDG in this screening system. 6-NBDG uptake in 3T3-L1 adipocytes was sensitive to insulin, known insulin mimetics, inhibitors of glucose transport and insulin-sensitizing compounds. To validate our screening system, a chemical library of 576 tagged, triazine-based small molecules was screened. The screening results were identical to that obtained from a commercial enzyme-based glucose assay. Two inducers of glucose uptake were shown to be non-cytotoxic and confirmed as insulin mimetic compounds by their inhibition of epinephrine-stimulated free fatty acid release from adipocytes. These novel insulin mimetics functioned at a markedly lower concentration than two widely studied insulin mimetics, zinc(II) complexes and vanadium compounds, and also showed novel, beneficial effects on endothelial cell function (a key determinant of secondary complications in diabetes). The discovery of new insulin mimetics using 6-NBDG validates the use of this probe in the development of large-scale, cell-based screening systems based on the uptake of fluorescent-tagged glucose analogues. This research should aid the development of novel strategies to discover new drugs and drug targets for combating the increasing prevalence of diabetes.

Stem cells, which are capable of self-renewing and differ-entiating into various types of cells, have captured greatinterest as a valuable resource for regenerative medicine anddevelopmental biology research. Technical progress duringthe last decade has enabled the isolation of stem cells from awide range of tissues, their differentiation into specific typesof cells, and the generation of induced pluripotent stem cells(iPSC) from somatic cells. The recent success of patient-specific iPSC generation

A major barrier to regeneration of CNS axons is the presence of growth-inhibitory proteins associated with myelin and the glial scar. To identify chemical compounds with the ability to overcome the inhibition of regeneration, we screened a novel triazine library, based on the ability of compounds to increase neurite outgrowth from cerebellar neurons on inhibitory myelin substrates. The screen produced four “hit compounds,” which act with nanomolar potency on several different neuronal types and on several distinct substrates relevant to glial inhibition. Moreover, the compounds selectively overcome inhibition rather than promote growth in general. The compounds do not affect neuronal cAMP levels, PKC activity, or EGFR (epidermal growth factor receptor) activation. Interestingly, one of the compounds alters microtubule dynamics and increases microtubule density in both fibroblasts and neurons. This same compound promotes regeneration of dorsal column axons after acute lesions and potentiates regeneration of optic nerve axons after nerve crushin vivo. These compounds should provide insight into the mechanisms through which glial-derived inhibitors of regeneration act, and could lead to the development of novel therapies for CNS injury.

Imaging a specific protein of interest in live cell has versatile applications in biological research. Recently, diverse chemical tags have been developed to overcome the limits of autofluorescence protein (FP) tags. However, current chemical methods still need to be progressed to compete with FPs in the scope of specificity and convenience in staining procedure. We report a novel protein tagging method that provides a convenient and specific fluorescent labeling of membrane proteins. Ω tag is developed by employing a mammalian enzyme glutathione sulfur-transferase omega 1 (GSTO1) and its partner dye, 5-bromomethyl fluorescein (BMF). Ω-tagged membrane proteins were labeled by BMF efficiently for live cell imaging and in-gel analysis. Endocytosis of epidermal growth factor receptor (EGFR) was successfully visualized by using this Ω tagging system. Ω tag will provide a convenient tool for the physiological study of membrane proteins in live cells.

Through organism based screening of a rosamine library using zebrafish larvae, novel neural tracers for live imaging were discovered with superior performance.

SummaryCarcinoma-associated fibroblasts (CAFs) promote tumor invasion by secreting soluble factors. A tagged triazine library was screened in our novel transwell coculture model of CAF and oral squamous cell carcinoma (OSCC). We discovered compound S06, which reduced OSCC invasion by inhibiting secretion of CAF-derived proinvasive chemokines. The N-terminus of Hsp90 was found to be the cellular target of S06. Importantly, S06 did not induce hepatic toxicity, a side effect associated with well-known Hsp90 inhibitors. Moreover, S06 inhibited tumor cell migration in a zebrafish xenograft model. Our results demonstrate that Hsp90 is a novel target for stromal-based therapy to modulate proinvasive molecular crosstalk within the tumor microenvironment. Furthermore, S06 represents a new class of Hsp90 inhibitor and is an attractive candidate for anticancer drug development.