The cancer-associated microprotein CASIMO1 controls cell proliferation and interacts with squalene epoxidase modulating lipid droplet formation.

Breast cancer is a leading cause of cancer-related death in women. Small open reading frame (sORF)-encoded proteins or microproteins constitute a new class of molecules often transcribed from presumed long non-coding RNA transcripts (lncRNAs). The translation of some of these sORFs has been confirmed, but their cellular function and importance remains largely unknown. Here, we report the identification and characterization of a novel microprotein of 10 kDa, which we named Cancer-Associated Small Integral Membrane Open reading frame 1 (CASIMO1). CASIMO1 RNA is overexpressed predominantly in hormone receptor-positive breast tumors. Its knockdown leads to decreased proliferation in multiple breast cancer cell lines. Its loss disturbs the organization of the actin cytoskeleton, leads to inhibition of cell motility, and causes a G0/G1 cell cycle arrest. The proliferation phenotype upon overexpression is observed only with CASIMO1 protein expression, but not with a non-translatable mutant attributing the effects to the sORF-derived protein rather than a lncRNA function. CASIMO1 microprotein interacts with squalene epoxidase (SQLE), a key enzyme in cholesterol synthesis and a known oncogene in breast cancer. Overexpression of CASIMO1 leads to SQLE protein accumulation without affecting its RNA levels and increased lipid droplet clustering, while knockdown of CASIMO1 decreased SQLE protein abundance and ERK phosphorylation downstream of SQLE. Importantly, SQLE knockdown mimicked the CASIMO1 knockdown phenotype and in turn SQLE overexpression fully rescued the effect of CASIMO1 knockdown. These findings establish CASIMO1 as the first functional microprotein that plays a role in carcinogenesis and is implicated in the cell lipid homeostasis.

Erratum to: The OECD validation program of the H295R steroidogenesis assay: Phase 3. Final inter-laboratory validation study.

In the original article wrong unites were quoted in Table 3 (page 508) and Table 4 (page 510) as well as in the paragraph 3.2 Core chemical exposure experiments on page 509. Also in paragraph 2.3 Selection and testing of chemicals the link to the Supplemental Materials (ESM) was missing.

Alternative splicing affects the subcellular localization of Drosha.

The RNase III enzyme Drosha is a key factor in microRNA (miRNA) biogenesis and as such indispensable for cellular homeostasis and developmental processes. Together with its co-factor DGCR8, it converts the primary transcript (pri-miRNA) into the precursor hairpin (pre-miRNA) in the nucleus. While the middle and the C-terminal domain are crucial for pri-miRNA processing and DGCR8 binding, the function of the N-terminus remains cryptic. Different studies have linked this region to the subcellular localization of Drosha, stabilization and response to stress. In this study, we identify alternatively spliced Drosha transcripts that are devoid of a part of the arginine/serine-rich (RS-rich) domain and expressed in a large set of human cells. In contrast to their expected habitation, we find two isoforms also present in the cytoplasm, while the other two isoforms reside exclusively in the nucleus. Their processing activity for pri-miRNAs and the binding to co-factors remains unaltered. In multiple cell lines, the endogenous mRNA expression of the Drosha isoforms correlates with the localization of endogenous Drosha proteins. The pri-miRNA processing efficiency is not significantly different between groups of cells with or without cytoplasmic Drosha expression. In summary, we discovered novel isoforms of Drosha with differential subcellular localization pointing toward additional layers of complexity in the regulation of its activity.

Sequence-engineered mRNA Without Chemical Nucleoside Modifications Enables an Effective Protein Therapy in Large Animals.

Being a transient carrier of genetic information, mRNA could be a versatile, flexible, and safe means for protein therapies. While recent findings highlight the enormous therapeutic potential of mRNA, evidence that mRNA-based protein therapies are feasible beyond small animals such as mice is still lacking. Previous studies imply that mRNA therapeutics require chemical nucleoside modifications to obtain sufficient protein expression and avoid activation of the innate immune system. Here we show that chemically unmodified mRNA can achieve those goals as well by applying sequence-engineered molecules. Using erythropoietin (EPO) driven production of red blood cells as the biological model, engineered Epo mRNA elicited meaningful physiological responses from mice to nonhuman primates. Even in pigs of about 20 kg in weight, a single adequate dose of engineered mRNA encapsulated in lipid nanoparticles (LNPs) induced high systemic Epo levels and strong physiological effects. Our results demonstrate that sequence-engineered mRNA has the potential to revolutionize human protein therapies.

Rare Drosha splice variants are deficient in microRNA processing but do not affect general microRNA expression in cancer cells.

Drosha is a key enzyme in microRNA biogenesis, generating the precursor miRNA (pre-miRNA) by excising the stem-loop embedded in the primary transcripts (pri-miRNA). The specificity for the pri-miRNAs and determination of the cleavage site are provided by its binding partner DGCR8, which is necessary for efficient processing. The crucial Drosha domains for pri-miRNA cleavage are the middle part, the two enzymatic RNase III domains (RIIID), and the dsRNA binding domain (dsRBD) in the C-terminus. Here, we identify alternatively spliced transcripts in human melanoma and NT2 cell lines, encoding C-terminally truncated Drosha proteins lacking part of the RIIIDb and the entire dsRBD. Proteins generated from these alternative splice variants fail to bind to DGCR8 but still interact with Ewing sarcoma protein (EWS). In vitro as well as in vivo, the Drosha splice variants are deficient in pri-miRNA processing. However, the aberrant transcripts in melanoma cells do not consistently reduce mature miRNA levels compared with melanoma cell lines lacking those splice variants, possibly owing to their limited abundance. Our findings show that alternative processing-deficient Drosha splice variants exist in melanoma cells. In elevated amounts, these alternatively spliced transcripts could provide one potential mechanism accounting for the deregulation of miRNAs in cancer cells. On the basis of our results, the search for alternative inactive splice variants might be fruitful in different tumor entities to unravel the molecular basis of the previously observed decreased microRNA processing efficiency in cancer.

Endocrine disrupting, mutagenic, and teratogenic effects of upper Danube River sediments using effect-directed analysis.

Effect-directed analysis (EDA) can be useful in identifying and evaluating potential toxic chemicals in matrixes. Previous investigations of extracts of sediments from the upper Danube River in Germany revealed acute nonspecific and mechanism-specific toxicity as determined by several bioassays. In the present study, EDA was used to further characterize these sediments and identify groups of potentially toxic chemicals. Four extracts of sediments were subjected to a novel fractionation scheme coupled with identification of chemicals to characterize their ability to disrupt steroidogenesis or cause mutagenic and/or teratogenic effects. All four whole extracts of sediment caused significant alteration of steroidogenesis and were mutagenic as well as teratogenic. The whole extracts of sediments were separated into 18 fractions and these fractions were then subjected to the same bioassays as the whole extracts. Fractions 7 to 15 of all four extracts were consistently more potent in both the Ames fluctuation and H295R assays. Much of this toxicity could be attributed to polycyclic aromatic hydrocarbons, sterols, and in fraction 7-naphthoic acids. Because the fraction containing polychlorinated biphenyls, polychlorodibenzodioxin/furan, dichlorodiphenyltrichloroethane, and several organophosphates did not cause any observable effects on hormone production or a mutagenic response, or were not detected in any of the samples, these compounds could be eliminated as causative agents for the observed effects. These results demonstrate the value of using EDA, which uses multiple bioassays and new fractionation techniques to assess toxicity. Furthermore, to our knowledge this is the first study using the recently developed H295R assay within EDA strategies.

Chlorinated isomers of nonylphenol differ in estrogenic and androgenic activity.

Technical mixtures of nonylphenol (NP) contain over 20 p-substituted isomers. Mono- and di-chlorinated derivatives are generated during the chlorination process in water treatment. Four NP isomers (i.e. 4n-, p353-, p33-, p363-NP) and their mono- (MCl) and di-chlorinated (DCl) derivatives were tested for their estrogenic and androgenic potency using yeast estrogenic and androgenic assay. The p353-NP and 4n-MClNP isomers showed the highest and the lowest estrogenic potency, respectively. The p363-MClNP exhibits estrogenic potency comparable to the parent isomer, whereas all p-DClNP compounds displayed a decrease in the estrogenic potency. In the anti-androgenic screen, all substances exhibited a positive response; the mono- and di-chlorinated derivatives exhibit lower potency than the parent isomers. The isomer p363-NP and its corresponding mono- and di-chlorinated derivatives were almost inactive. Furthermore, all compounds were tested for anti-estrogenic and androgenic assays, but none of them showed a positive response. These results indicate that for assessing the xeno-hormone potency of chlorinated derivatives of NP, the use of pure compounds is essential because the mixtures are not representative. In fact the concentrations of NP isomers differ in technical mixtures according to the producers; after chlorination different technical mixtures can generate dissimilar ratios of chlorinated derivatives. Finally, the chlorinated derivatives of NP didn't show an increase in xeno-hormone potency compared to the parent isomers, and for this reason the many oxidized by-products generated during chlorination process mask the xeno-hormone potency of the pure chlorinated isomers of NP.

The OECD validation program of the H295R steroidogenesis assay: Phase 3. Final inter-laboratory validation study.

UNLABELLED: BACKGROUND, GOALS, AND SCOPE: In response to increasing concerns regarding the potential of chemicals to interact with the endocrine system of humans and wildlife, various national and international programs have been initiated with the aim to develop new guidelines for the screening and testing of these chemicals in vertebrates. Here, we report on the validation of an in vitro assay, the H295R steroidogenesis assay, to detect chemicals with the potential to inhibit or induce the production of the sex steroid hormones testosterone (T) and 17ß-estradiol (E2) in preparation for the development of an Organization for Economic Cooperation and Development (OECD) test guideline. METHODS: A previously optimized and pre-validated protocol was used to assess the potential of 28 chemicals of diverse structures and properties to validate the H295R steroidogenesis assay. These chemicals are comprised of known endocrine-active chemicals and "negative" chemicals that were not expected to have effects on the targeted endpoints, as well as a number of test chemicals with unknown modes of action at the level of the steroidogenic pathway. A total of seven laboratories from seven countries participated in this effort. In addition to effects on hormone production, confounding factors, such as cell viability and possible direct interference of test substances with antibody-based hormone detection assays, were assessed. Prior to and during the conduct of exposure experiments, each laboratory had to demonstrate that they were able to conduct the assay within the margin of predefined performance criteria. RESULTS: With a few exceptions, all laboratories met the key quality performance parameters, and only 2% and 7% of all experiments for T and E2, respectively, were excluded due to exceedance of these parameters. Of the 28 chemicals analyzed, 13 and 14 tested affected production of T and E2, respectively, while 11 and 8 did not result in significant effects on T and E2 production, respectively. Four and six chemicals produced ambiguous results for effects on T and E2 production, respectively. However, four of these cases each for T and E2 were associated with only one laboratory after a personnel change occurred. Significant interference of test chemicals with some of the antibody-based hormone detection systems occurred for four chemicals. Only one of these chemicals, however, significantly affected the ability of the detection system to categorize the chemical as affecting E2 or T production. DISCUSSION AND CONCLUSIONS: With one exception, the H295R steroidogenesis assay protocol successfully identified the majority of chemicals with known and unknown modes of interaction as inducers or inhibitors of T and E2 production. Thus it can be considered a reliable screen for chemicals that can alter the production of sex steroid hormones. One of the remaining limitations associated with the H295R steroidogenesis assay protocol is the relatively small basal production of E2 and its effect on quantifying the decreased production of this hormone with regard to the identification of weak inhibitors. An initial comparison of the data produced in this study with those from in vivo studies from the literature demonstrated the potential of the H295R steroidogenesis assay to identify chemicals affecting hormone homeostasis in whole organisms. Particularly promising was the lack of any false negatives during the validation and the very low number of false positives (1 out of 28 chemicals for each T and E2). PERSPECTIVES: Based on the results obtained during this validation study and the accordingly revised test protocols, an OECD draft test guideline was developed and submitted to the OECD working group of the national coordinators of the test guidelines program (WNT) for comments in December 2009.

The endocrine disrupting potential of sediments from the Upper Danube River (Germany) as revealed by in vitro bioassays and chemical analysis.

INTRODUCTION: The present study was part of a comprehensive weight-of-evidence approach with the goal of identifying potential causes for the declines in fish populations, which have been observed during the past decades in the Upper Danube River. METHODS: The specific goal was the investigation of the endocrine disrupting potential of sediment extracts from different sites along the Danube River. Parallel to the identification and quantification of target estrogens, two in vitro bioassays were employed to assess the estrogenic potential (yeast estrogen screen, YES) of the sediment samples and to evaluate their effects on the production of testosterone (T) and E2 (H295R Steroidogenesis Assay). Using a potency balance approach, the contribution of the measured compounds (Chem-EEQs) to the total endocrine activity measured by the YES (YES-EEQs) was calculated. RESULTS AND DISCUSSION: Of the nine sediment extracts tested five extracts exhibited significant estrogenic activities in the YES, which suggested the presence of ER agonists in these samples. The xenoestrogens nonylphenol (NP) and bisphenol A (BPA) and the natural estrogen estrone (E1) were detected while concentrations of 17ß-estradiol (E2) and ethinylestradiol (EE2) were less than their respective limits of quantification in all sediment extracts. A comparison of the measured YES-EEQs and the calculated Chem-EEQs revealed that as much as 6% of estrogenic activity in extracts of most sediments could be explained by two xeno- and one natural estrogen. Exposure of H295R cells to sediment extracts from four different locations in the Danube River resulted in significantly increased concentrations of E2, but only slight inhibition of T synthesis. Furthermore, application of the H295R Steroidogenesis Assay provided evidence for endocrine disrupting potencies in sediment samples from the Upper Danube River, some of which were not detectable with the YES. In conclusion, differential endocrine activities were associated with several sediments from the Upper Danube River. Further investigations will have to show whether the observed activities are of biological relevance with regard to declines in fish populations in the Upper Danube River.

Comparison of in vitro and in situ genotoxicity in the Danube River by means of the comet assay and the micronucleus test.

Genotoxicity can be correlated with adverse reproductive effects or may even result in elevated extinction risk for particular species of an ecosystem. It may thus be a valuable tool for screening of pollution and potential environmental harm. Since many genotoxicants tend to adsorb onto particulate matter, sediments and suspended materials are of particular interest for genotoxicity screening under field conditions. In order to correlate the genotoxic potential of sediments with genetic damage in fish, rainbow-trout liver (RTL-W1) cells were exposed in vitro to acetone extracts of sediments collected at 10 selected sites along the upper Danube River and analyzed in the comet and micronucleus assays. These in vitro results were compared with micronucleus formation in erythrocytes of the European barbel (Barbus barbus) caught in the field. The two in vitro bioassays showed excellent correlation, indicating comparability of genotoxic potentials in vitro. Sampling sites could be clearly differentiated with respect to severity of effects, with Rottenacker as the most heavily contaminated site, Ehingen and Schwarzach as moderately genotoxic, and with the weakest effects in the tributary Lauchert. All other sediment extracts showed intermediate genotoxic or clastogenic effects. In situ, micronucleus formation in barbel erythrocytes indicated severe genotoxicity at Rottenacker, moderate effects at Ehingen, but minor contamination at Riedlingen and Sigmaringen. In situ observations thus showed excellent correlation with corresponding in vitro tests and document the ecological relevance of in vitro studies with sediment extracts. With respect to the ecological status of the Danube River, the results overall indicate a moderate to severe genotoxic potential with a highly differential localization.

Assessment of fish health status in the Upper Danube River by investigation of ultrastructural alterations in the liver of barbel Barbus barbus.

Despite intensive efforts and tightened guidelines for improvement of water quality over the last 2 decades, declines of fish populations have been reported for several rivers around the world. The present study forms part of a comprehensive weight-of-evidence approach, which aims to identify potential causes for the decline in fish catches observed in the Upper Danube River. The major focus of the present study is the investigation of the health status of wild barbel Barbus barbus L. collected from 3 locations along the Danube River, which experienced different levels of contamination. Whereas the comparison of the condition factor (CF) of field fish with that of control fish revealed no differences, ultrastructural investigations indicated severe disturbance of hepatic cell metabolism in field fish from the more contaminated sites Rottenacker and Ehingen, compared to both control fish and field fish from the less contaminated site Riedlingen. The ultrastructural analysis provided information about reactions of e.g. the rough endoplasmic reticulum, peroxisomes, and mitochondria, indicating an impaired health status of barbel at the sampling sites Rottenacker and Ehingen. Even though a straightforward cause-effect relationship between sediment contamination and ultrastructural alterations could not be established, based on a meta-analysis and toxicity assays it may be suggested that sediment-bound xenobiotics at least partly account for the hepatocellular changes. A relationship between impaired fish health status and the decline of fish catches along the Upper Danube River cannot be excluded.

The inner nuclear membrane protein Src1 associates with subtelomeric genes and alters their regulated gene expression.

Inner nuclear membrane proteins containing a LEM (LAP2, emerin, and MAN1) domain participate in different processes, including chromatin organization, gene expression, and nuclear envelope biogenesis. In this study, we identify a robust genetic interaction between transcription export (TREX) factors and yeast Src1, an integral inner nuclear membrane protein that is homologous to vertebrate LEM2. DNA macroarray analysis revealed that the expression of the phosphate-regulated genes PHO11, PHO12, and PHO84 is up-regulated in src1Delta cells. Notably, these PHO genes are located in subtelomeric regions of chromatin and exhibit a perinuclear location in vivo. Src1 spans the nuclear membrane twice and exposes its N and C domains with putative DNA-binding motifs to the nucleoplasm. Genome-wide chromatin immunoprecipitation-on-chip analyses indicated that Src1 is highly enriched at telomeres and subtelomeric regions of the yeast chromosomes. Our data show that the inner nuclear membrane protein Src1 functions at the interface between subtelomeric gene expression and TREX-dependent messenger RNA export through the nuclear pore complexes.

Activities and identification of aryl hydrocarbon receptor agonists in sediments from the Danube river.

This study is a consequence of a distinct fish decline in the Danube river since the beginning of the 1990s. In contrast to the decline of fish population, former studies have repeatedly documented that the water quality along the Danube river is improving. However, the conclusion of a pilot study in 2002 was that a high hazard potential is associated with local sediments. The present study documents that sediment samples from the Danube river showed comparatively high aryl hydrocarbon receptor mediated activity in biotests, using the cell lines GPC.2D.Luc, H4IIE (DR-CALUX) and RTL-W1. The combination of chemical analysis, fractionation techniques and different in vitro tests revealed that priority pollutants could not explain the main induction, even though the concentrations of priority polycyclic aromatic hydrocarbons (PAHs) were very high (maximum in the tributary Schwarzach, sum of 16 EPA PAHs 26 mug/g). In conclusion, this investigation shows that nonpriority pollutants mainly mediate the high induction rates. Nevertheless, owing to the effects of PAHs towards fish and the connection between dioxin-like activity and carcinogenicity, the link between contamination and the fish population decline cannot be ruled out.