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Human telomerase reverse transcriptase (hTERT; the catalytic protein subunit of telomerase) is subjected to numerous alternative splicing events, but the regulation and function of these splice variants is obscure. Full-length hTERT includes conserved domains that encode reverse transcriptase activity, RNA binding, and other functions. The major splice variant termed α+β− or β-deletion is highly expressed in stem and cancer cells, where it codes for a truncated protein lacking most of the reverse transcriptase domain but retaining the known RNA-binding motifs. In a breast cancer cell panel, we found that β-deletion was the hTERT transcript that was most highly expressed. Splicing of this transcript was controlled by the splice regulators SRSF11, HNRNPH2, and HNRNPL, and the β-deletion transcript variant was associated with polyribosomes in cells. When ectopically overexpressed, β-deletion protein competed for binding to telomerase RNA (hTR/TERC), thereby inhibiting endogenous telomerase activity. Overexpressed β-deletion protein localized to the nucleus and mitochondria and protected breast cancer cells from cisplatin-induced apoptosis. Our results reveal that a major hTERT splice variant can confer a growth advantage to cancer cells independent of telomere maintenance, suggesting that hTERT makes multiple contributions to cancer pathophysiology. Cancer Res; 73(9); 2817–28. ©2013 AACR.

PDF file - 516K, T1. Breast cell lines used in this study. T2. Summary of results for 45 breast cancer cell lines and 5 non-malignant cell lines. T3. Correlation of hTERT α/β splice variants, telomerase activity, telomere length and hTR in 50 breast cancer cell lines. T4. Sequences of primers used.

PDF file - 236K, S1. hTERT and SRSF3 splice variant enrichment after cycloheximide treatment. S2. Total SRSF3 and hTERT splice variant mRNA abundance in ribosome-containing fractions. S3. Unaltered microscopy image shown in Figure 3. S4. SRSF11 and hnRNPH2 binding sites in pSpliceExpress-hTERT. S5. hTR 3' end co-immunoprecipitates with FLAG-WT-hTERT, FLAG-D868A-hTERT and FLAG-β-deletion. S6. hTERT detection by Western blot in UM-UC-3 lysates from experiment 5C. S7. hTR RNA expression levels in breast cancer cell lines. S8. Modal telomere length stayed relatively constant after 20 continues passages in randomly selected breast cell lines. S9. Telomerase activity and relative expression of hTERT α+β+ and β-deletion mRNAs in breast cancer cell line subtypes.

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Canonically, complement is a serum-based host defense system that protects against systemic microbial invasion. Little is known about the production and function of complement components on mucosal surfaces. Here we show gut complement component 3 (C3), central to complement function, is regulated by the composition of the microbiota in healthy humans and mice, leading to host-specific gut C3 levels. Stromal cells in intestinal lymphoid follicles (LFs) are the predominant source of intestinal C3. During enteric infection withCitrobacter rodentiumor enterohemorrhagicEscherichia coli,luminal C3 levels increase significantly and are required for protection.C. rodentiumis remarkably more invasive to the gut epithelium of C3-deficient mice than of wild-type mice. In the gut, C3-mediated phagocytosis ofC. rodentiumfunctions to clear pathogens. Our study reveals that variations in gut microbiota determine individuals’ intestinal mucosal C3 levels, dominantly produced by LF stromal cells, which directly correlate with protection against enteric infection.HighlightsGut complement component 3 (C3) is induced by the microbiome in healthy humans and mice at a microbiota-specific level.Gut stromal cells located in intestinal lymphoid follicles are a major source of luminal C3During enteric infections withCitrobacter rodentiumor enterohemorrhagicEscherichia coli,gut luminal C3 levels increase and are required for protection.C. rodentiumis significantly more invasive of the gut epithelium in C3-deficient mice when compared to WT mice.In the gut, C3-mediated opsonophagocytosis ofC. rodentiumfunctions to clear pathogens.

Recently in Cell Metabolism, Challapa et al. used isotope labeling to track NAD metabolism in host tissues and the gut microbiota. They describe a symbiotic relationship in which the gut microbiota uses host-derived nicotinamide to generate NAD and in return, produces nicotinic acid for host NAD biosynthesis.

It is impossible to analyze human-specific host-microbiome interactions using animal models and existing in vitro methods fail to support survival of human cells in direct contact with complex living microbiota for extended times. Here we describe a protocol for culturing human organ-on-a-chip (Organ Chip) microfluidic devices lined by human patient-derived primary intestinal epithelium in the presence of a physiologically relevant transluminal hypoxia gradient that enables their coculture with hundreds of different living aerobic and anaerobic bacteria found within the human gut microbiome. This protocol can be adapted to provide different levels of oxygen tension to facilitate coculturing of microbiome from different regions of gastrointestinal tract, and the same system can be applied with any other type of Organ Chip. This method can help to provide further insight into the host-microbiome interactions that contribute to human health and disease, enable discovery of new microbiome-related diagnostics and therapeutics, and provide a novel approach to advanced personalized medicine.

It is impossible to analyze human-specific host-microbiome interactions using animal models and existing in vitro methods fail to support survival of human cells in direct contact with complex living microbiota for extended times. Here we describe a protocol for culturing human organ-on-a-chip (Organ Chip) microfluidic devices lined by human patient-derived primary intestinal epithelium in the presence of a physiologically relevant transluminal hypoxia gradient that enables their coculture with hundreds of different living aerobic and anaerobic bacteria found within the human gut microbiome. This protocol can be adapted to provide different levels of oxygen tension to facilitate coculturing of microbiome from different regions of gastrointestinal tract, and the same system can be applied with any other type of Organ Chip. This method can help to provide further insight into the host-microbiome interactions that contribute to human health and disease, enable discovery of new microbiome-related diagnostics and therapeutics, and provide a novel approach to advanced personalized medicine.

The mammalian immune system is tolerized to trillions of microbes residing on bodily surfaces and can discriminate between symbionts and pathogens despite their having related microbial structures. Mechanisms of innate immune activation and the subsequent signaling pathways used by symbionts to communicate with the adaptive immune system are poorly understood. Polysaccharide A (PSA) of Bacteroides fragilis is the model symbiotic immunomodulatory molecule. Here we demonstrate that PSA-dependent immunomodulation requires the Toll-like receptor (TLR) 2/1 heterodimer in cooperation with Dectin-1 to initiate signaling by the downstream phosphoinositide 3-kinase (PI3K) pathway, with consequent CREB-dependent transcription of antiinflammatory genes, including antigen presentation and cosignaling molecules. High-resolution LC-MS/MS analysis of PSA identified a previously unknown small molecular-weight, covalently attached bacterial outer membrane-associated lipid that is required for activation of antigen-presenting cells. This archetypical commensal microbial molecule initiates a complex collaborative integration of Toll-like receptor and C-type lectin-like receptor signaling mechanisms culminating in the activation of the antiinflammatory arm of the PI3K pathway that serves to educate CD4(+) Tregs to produce the immunomodulatory cytokine IL-10. Immunomodulation is a key function of the microbiome and is a focal point for developing new therapeutic agents.

The diverse bacterial populations that comprise the commensal microbiota of the human intestine play a central role in health and disease, yet no method is available to sustain these complex microbial communities in direct contact with living human intestinal cells and their overlying mucus layer in vitro. Here we describe a human Organ-on-a-Chip (Organ Chip) microfluidic platform that permits control and real-time assessment of physiologically-relevant oxygen gradients, and which enables co-culture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota. When compared to aerobic co-culture conditions, establishment of a transluminal hypoxia gradient sustained higher microbial diversity with over 200 unique operational taxonomic units (OTUs) from 11 different genera, and an abundance of obligate anaerobic bacteria with ratios of Firmicutes and Bacteroidetes similar to those observed in human feces, in addition to increasing intestinal barrier function. The ability to culture human intestinal epithelium overlaid by complex human gut microbial communities within microfluidic Intestine Chips may enable investigations of host-microbiome interactions that were not possible previously, and serve as a discovery tool for development of new microbiome-related therapeutics, probiotics, and nutraceuticals.

The diverse bacterial populations that comprise the commensal microbiome of the human intestine play a central role in health and disease. A method that sustains complex microbial communities in direct contact with living human intestinal cells and their overlying mucus layer in vitro would thus enable the investigation of host-microbiome interactions. Here, we show the extended coculture of living human intestinal epithelium with stable communities of aerobic and anaerobic human gut microbiota, using a microfluidic intestine-on-a-chip that permits the control and real-time assessment of physiologically relevant oxygen gradients. When compared to aerobic coculture conditions, the establishment of a transluminal hypoxia gradient in the chip increased intestinal barrier function and sustained a physiologically relevant level of microbial diversity, consisting of over 200 unique operational taxonomic units from 11 different genera and an abundance of obligate anaerobic bacteria, with ratios of Firmicutes and Bacteroidetes similar to those observed in human faeces. The intestine-on-a-chip may serve as a discovery tool for the development of microbiome-related therapeutics, probiotics and nutraceuticals.

Telomerase is a ribonucleoprotein complex that adds telomeric DNA to the ends of linear chromosomes. It contains two core canonical components: the essential RNA component, hTR, which provides the template for DNA synthesis, and the reverse transcriptase protein component, hTERT. Low telomerase activity in circulating peripheral blood mononuclear cells has been associated with a variety of diseases. It is unknown, however, whether telomerase, in addition to its long-term requirement for telomere maintenance, is also necessary for short-term immune cell proliferation and survival. We report that overexpression of enzymatically inactive hTR mutants protected against dexamethasone-induced apoptosis in stimulated CD4 T cells. Furthermore, hTR knockdown reproducibly induced apoptosis in the absence of any detectable telomere shortening or DNA damage response. In contrast, hTERT knockdown did not induce apoptosis. Strikingly, overexpression of hTERT protein caused apoptosis that was rescued by overexpression of enzymatically inactive hTR mutants. Hence, we propose that hTR can function as a noncoding RNA that protects from apoptosis independent of its function in telomerase enzymatic activity and long-term telomere maintenance in normal human immune cells. These results imply that genetic or environmental factors that alter hTR levels can directly affect immune cell function to influence health and disease.

In the version of this Article originally published, the authors mistakenly cited Fig. 5d in the sentence beginning ‘Importantly, the microbiome cultured in these primary Intestine Chips...’; the correct citation is Supplementary Table 2. This has now been amended.

Wild mice are genetically similar to laboratory mice, but have a distinct gut microbiota that protects from disease.

NAD+ is a co-enzyme for hydride transfer enzymes and an essential substrate of ADP-ribose transfer enzymes and sirtuins, the type III protein lysine deacetylases related to yeast Sir2. Supplementation of yeast cells with nicotinamide riboside extends replicative lifespan and increases Sir2-dependent gene silencing by virtue of increasing net NAD+ synthesis. Nicotinamide riboside elevates NAD+ levels via the nicotinamide riboside kinase pathway and by a pathway initiated by splitting the nucleoside into a nicotinamide base followed by nicotinamide salvage. Genetic evidence has established that uridine hydrolase, purine nucleoside phosphorylase, and methylthioadenosine phosphorylase are required for Nrk-independent utilization of nicotinamide riboside in yeast. Here we show that mammalian purine nucleoside phosphorylase but not methylthioadenosine phosphorylase is responsible for mammalian nicotinamide riboside kinase-independent nicotinamide riboside utilization. We demonstrate that so-called uridine hydrolase is 100-fold more active as a nicotinamide riboside hydrolase than as a uridine hydrolase and that uridine hydrolase and mammalian purine nucleoside phosphorylase cleave nicotinic acid riboside, whereas the yeast phosphorylase has little activity on nicotinic acid riboside. Finally, we show that yeast nicotinic acid riboside utilization largely depends on uridine hydrolase and nicotinamide riboside kinase and that nicotinic acid riboside bioavailability is increased by ester modification.

Despite the accepted health benefits of consuming dietary fiber, little is known about the mechanisms by which fiber deprivation impacts the gut microbiota and alters disease risk. Using a gnotobiotic mouse model, in which animals were colonized with a synthetic human gut microbiota composed of fully sequenced commensal bacteria, we elucidated the functional interactions between dietary fiber, the gut microbiota and the colonic mucus barrier, which serves as a primary defense against enteric pathogens. We show that during chronic or intermittent dietary fiber deficiency, the gut microbiota resorts to host-secreted mucus glycoproteins as a nutrient source, leading to erosion of the colonic mucus barrier. Dietary fiber deprivation, together with a fiber-deprived, mucus-eroding microbiota, promotes greater epithelial access and lethal colitis by the mucosal pathogen, Citrobacter rodentium. Our work reveals intricate pathways linking diet, the gut microbiome and intestinal barrier dysfunction, which could be exploited to improve health using dietary therapeutics.

Telomerase canonically maintains telomeres, but recent reports have suggested that the core protein mammalian telomerase reverse transcriptase (TERT) component, together with the chromatin remodeling factor BRG1 and β-catenin, may also bind to and promote expression of Wnt target genes. However, this proposed noncanonical role of TERT in Wnt signaling has been controversial. Here, we investigated the effects of human TERT (hTERT) on Wnt signaling in human breast cancer lines and HeLa cells. We failed to find evidence for physical association of hTERT with BRG1 or β-catenin; instead, we present evidence that anti-FLAG antibody cross-reactivity properties may explain the previously reported interaction of hTERT with β-catenin. Furthermore, altering hTERT levels in four different breast cancer cell lines caused minimal and discordant effects on Wnt target and Wnt pathway gene expression. Although hTERT's role in Wnt signaling was addressed only indirectly, no significant representation of Wnt target genes was detected in chromatin immunoprecipitation-sequencing (ChIP-seq) and chromatin isolation by RNA purification and sequencing (ChIRP-seq) loci cooccupied in HeLa S3 cells by both BRG1 and hTR. In summary, our evidence fails to support the idea of a biologically consistent hTERT interaction with the Wnt pathway in human breast cancer cells, and any detectable influence of hTERT depended on cell type and experimental system.

Human telomerase reverse transcriptase (hTERT; the catalytic protein subunit of telomerase) is subjected to numerous alternative splicing events, but the regulation and function of these splice variants is obscure. Full-length hTERT includes conserved domains that encode reverse transcriptase activity, RNA binding, and other functions. The major splice variant termed α+β− or β-deletion is highly expressed in stem and cancer cells, where it codes for a truncated protein lacking most of the reverse transcriptase domain but retaining the known RNA-binding motifs. In a breast cancer cell panel, we found that β-deletion was the hTERT transcript that was most highly expressed. Splicing of this transcript was controlled by the splice regulators SRSF11, HNRNPH2, and HNRNPL, and the β-deletion transcript variant was associated with polyribosomes in cells. When ectopically overexpressed, β-deletion protein competed for binding to telomerase RNA (hTR/TERC), thereby inhibiting endogenous telomerase activity. Overexpressed β-deletion protein localized to the nucleus and mitochondria and protected breast cancer cells from cisplatin-induced apoptosis. Our results reveal that a major hTERT splice variant can confer a growth advantage to cancer cells independent of telomere maintenance, suggesting that hTERT makes multiple contributions to cancer pathophysiology. Cancer Res; 73(9); 2817–28. ©2013 AACR.

Neurogenetics (2009) 10:169–170 DOI 10.1007/s10048-009-0180-6 LETTER TO THE EDITORS Reply to the “Letter to the Editors” by Steven Buyske K. Abu-Elneel & T. Liu & F. S. Gazzaniga & Y. Nishimura & D. P. Wall & D. H. Geschwind & K. Lao & K. S. Kosik Received: 26 January 2009 / Accepted: 26 January 2009 / Published online: 24 February 2009 # The Author(s) 2009. This article is published with open access at Springerlink.com Dear Editors: We appreciate the opportunity to clarify the statistical treatment of our data. During the preparation of the manuscript, we did consider the use of the t-test as proposed by Dr. Buyske. Indeed, the z-test requires that the standard deviation be known, while we estimated the standard deviation from the sample. However, the t-test is not ideal either. A t-test compares two groups of values and the statistics rely on the standard deviation of both groups. It is unconventional to use the t-test to compare a single value, i.e., that of the miRNA in each case of autism against a group of values. By definition, the single values do not K. Abu-Elneel : T. Liu : F. S. Gazzaniga : K. S. Kosik (*) Neuroscience Research Institute, Department of Molecular Cellular and Developmental Biology, University of California Santa Barbara, Santa Barbara, CA 93106, USA e-mail: kosik@lifesci.ucsb.edu Y. Nishimura : D. H. Geschwind Department of Neurology, David Geffen School of Medicine, University of California at Los Angeles, Los Angeles, CA 90095-1769, USA D. P. Wall The Center for Biomedical Informatics & Department of Systems Biology, Harvard Medical School, Boston, MA 02115, USA K. Lao Applied Biosystems, 850 Lincoln Centre Dr., Foster City, CA 94404, USA Present Address: F. S. Gazzaniga Biomedical Sciences, University of California San Francisco, San Francisco, CA 94143, USA have a standard deviation. For this reason, we chose the z- test as a first-level less stringent screen to assess differential expression between one autistic case and 13 normal cases for each miRNA. We had also addressed the issue raised by Dr. Buyske with a nonparametric approach—the Wilcoxon rank test. However, the statistical power of the rank order test is rather weak and, more importantly, we lose the information in the differences in magnitude of the miRNAs. A strength of the method we used to profile the miRNAs—real-time PCR—is its ability to detect a broad dynamic range of miRNA expression. Our method was preferable to capture this quantitative parameter. However, the miRNAs with p- values that rank among the top using the parametric test remain among the top with the nonparametric test. The statistical testing as suggested by Dr. Buyske does demonstrate some differentially expressed miRNAs. With a one-sided t-test, our top five miRNAs remained statistically significant. The main difference between the z-test and t- test in a sense is the p-value cutoff. The z-test is indeed less stringent than the t-test and the two-sided t-test further increases the stringency. On the other hand, the Bonferroni correction for multiple hypotheses testing, applied in the manuscript, is often considered overly stringent. If we control for multiple hypotheses with a 5% false discovery rate (FDR) rather than the Bonferroni correction on t- statistics, the number of dysregulated miRNAs goes from five to 13. One could further argue that even the FDR is overly stringent because many miRNAs are co-regulated, and therefore treating each as an independent query may be unnecessarily conservative. Whichever the test and correction, we did provide all p- values signifying the difference between each autistic case and the normal cases for each miRNA, and these p-values are not affected by the significance cutoff. These p-values

microRNAs (miRNAs) are approximately 21 nt transcripts capable of regulating the expression of many mRNAs and are abundant in the brain. miRNAs have a role in several complex diseases including cancer as well as some neurological diseases such as Tourette's syndrome and Fragile x syndrome. As a genetically complex disease, dysregulation of miRNA expression might be a feature of autism spectrum disorders (ASDs). Using multiplex quantitative polymerase chain reaction (PCR), we compared the expression of 466 human miRNAs from postmortem cerebellar cortex tissue of individuals with ASD (n = 13) and a control set of non-autistic cerebellar samples (n = 13). While most miRNAs levels showed little variation across all samples suggesting that autism does not induce global dysfunction of miRNA expression, some miRNAs among the autistic samples were expressed at significantly different levels compared to the mean control value. Twenty-eight miRNAs were expressed at significantly different levels compared to the non-autism control set in at least one of the autism samples. To validate the finding, we reversed the analysis and compared each non-autism control to a single mean value for each miRNA across all autism cases. In this analysis, the number of dysregulated miRNAs fell from 28 to 9 miRNAs. Among the predicted targets of dysregulated miRNAs are genes that are known genetic causes of autism such Neurexin and SHANK3. This study finds that altered miRNA expression levels are observed in postmortem cerebellar cortex from autism patients, a finding which suggests that dysregulation of miRNAs may contribute to autism spectrum phenotype.

Abstract SCI-40 The ribonucleoprotein enzyme telomerase, which counteracts telomere shortening by adding telomeric DNA repeats to the 3’ ends of chromosomes, contains a core protein reverse transcriptase (called hTERT in humans), the essential template-containing RNA (hTER) and associated factors. Thus, telomerase is capable of circumventing the limit on cell division imposed by telomere attrition. Telomerase enzymatic activity is readily detectable in stem and progenitor cell populations, but is largely downregulated in most adult somatic human cells. In contrast, telomerase is highly active in the large majority (∼80%–90%) of cancer cells. While telomerase is essential for telomere maintenance in cells in vitro and in vivo, several studies now also indicate that telomerase may have telomere-independent functions. We previously showed that lowering the level of the telomerase ribonucleoprotein (RNP) enzyme complex causes rapid changes in cell cycle program in human and mouse cancer cells: partial reduction of telomerase induced by directly lowering telomerase RNP component levels causes altered transcriptional profiles and reduced glucose metabolism in human cancer cells, yet bulk telomere shortening or detectable telomere uncapping are not required for these effects. Work by others has shown that reduction of telomerase core protein component level reduced Wnt signaling and caused Wnt-mutant like developmental defects in Xenopus and mouse and aberrant hematopoiesis in zebrafish embryos. We acutely depleted telomerase RNA components in cultured T cells from healthy human adults using shRNAs targeting both the telomerase protein and the RNA component of telomerase (hTR), delivered immediately after in vitro stimulation. Cell proliferation and telomerase activity levels were quantified through the first and second stimulation cycles. Effects of such telomerase RNP reduction on cell proliferation were observed in time frames too short to be accounted for by bulk telomere attrition. Models to account for these findings will be discussed. Disclosures: Lin: Telome Health, Inc.: Consultancy, Equity Ownership. Blackburn:Telome Health, Inc: Equity Ownership, Membership on an entity’s Board of Directors or advisory committees.

Telomerase is a ribonucleoprotein complex that adds TTAGGG repeats to telomeres in a highly regulated fashion. Telomerase activity is absent in normal somatic cells, thus limiting their number of cell divisions due to telomere shortening. In contrast, the large majority of tumor cells upregulate telomerase activity, consistent with their ability to maintain stable telomere lengths and to divide indefinitely. Telomerase activity is detectable in over 90% of breast tumors, and it is well established that telomerase overexpression is an important step in the progression of normal epithelium to invasive breast cancer. In addition to telomerase upregulation, deregulation of various signaling pathways promotes tumor progression and metastasis. To better understand in which cellular pathway telomerase and telomeres are involved, we comprehensively quantified telomerase activity and telomere length in a panel of 52 extensively characterized breast cancer cell lines and correlated these metrics with the expression profiles of the cell lines. Across the entire panel of breast cancer cell lines, expression of 530 genes was significantly correlated with telomerase activity (FDR-corrected p-val < 0.2), while expression of 585 genes was significantly correlated with telomere length. Secondary G0-term analysis revealed that telomere length was significantly associated with genes involved in Alzheimer's disease, apoptosis regulation and negative regulation of transcription. Genes significantly correlated with telomerase activity were associated with apoptosis regulation, DNA repair, nucleotide metabolism and Wnt signaling. Several Wnt target genes, including MYC, KLF5, and FGF18 were also correlated with telomerase activity. We also used the network analysis tool PARADIGM (1) to identify cellular pathways associated with telomerase activity and telomere length. Notably, Wnt signaling components were significantly correlated with telomerase activity. Given the recent evidence that the telomerase component TERT can act as a transcriptional modulator of the Wnt/beta-catenin signaling pathway (2), we are currently testing how Wnt signaling is altered due to telomerase perturbation in breast cancer cells. (1) Vaske, C. J. et al. Inference of patient-specific pathway activities from multi-dimensional cancer genomics data using PARADIGM. Bioinformatics 2010; 26:i237–245 (2) Park, J. I. et al. Telomerase modulates Wnt signaling by association with target gene chromatin. Nature 2009; 460:66–72 Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the Second AACR International Conference on Frontiers in Basic Cancer Research; 2011 Sep 14-18; San Francisco, CA. Philadelphia (PA): AACR; Cancer Res 2011;71(18 Suppl):Abstract nr A58.