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Huggins, IJ, Bos T, Gaylord O, Jessen C, Lonquich B, Puranen A, Richter J, Rossdam C, Brafman D, Gaasterland T, Willert K.  2017.  The WNT target SP5 negatively regulates WNT transcriptional programs in human pluripotent stem cells. Nature Communications. 8   10.1038/s41467-017-01203-1   AbstractWebsite

The WNT/beta-catenin signaling pathway is a prominent player in many developmental processes, including gastrulation, anterior-posterior axis specification, organ and tissue development, and homeostasis. Here, we use human pluripotent stem cells (hPSCs) to study the dynamics of the transcriptional response to exogenous activation of the WNT pathway. We describe a mechanism involving the WNT target gene SP5 that leads to termination of the transcriptional program initiated by WNT signaling. Integration of gene expression profiles of wild-type and SP5 mutant cells with genome-wide SP5 binding events reveals that SP5 acts to diminish expression of genes previously activated by the WNT pathway. Furthermore, we show that activation of SP5 by WNT signaling is most robust in cells with developmental potential, such as stem cells. These findings indicate a mechanism by which the developmental WNT signaling pathway reins in expression of transcriptional programs.

Dickey, AS, Pineda VV, Tsunemi T, Liu PP, Miranda HC, Gilmore-Hall SK, Lomas N, Sampat KR, Buttgereit A, Torres MJM, Flores AL, Arreola M, Arbez N, Akimov SS, Gaasterland T, Lazarowski ER, Ross CA, Yeo GW, Sopher BL, Magnuson GK, Pinkerton AB, Masliah E, La Spada AR.  2016.  PPAR-delta is repressed in Huntington's disease, is required for normal neuronal function and can be targeted therapeutically. Nature Medicine. 22:37-+.   10.1038/nm.4003   AbstractWebsite

Huntington's disease (HD) is a progressive neurodegenerative disorder caused by a CAG trinucleotide repeat expansion in the huntingtin (HTT) gene, which encodes a polyglutamine tract in the HTT protein. We found that peroxisome proliferator-activated receptor delta (PPAR-delta) interacts with HTT and that mutant HTT represses PPAR-delta-mediated transactivation. Increased PPAR-delta transactivation ameliorated mitochondrial dysfunction and improved cell survival of neurons from mouse models of HD. Expression of dominant-negative PPAR-delta in the central nervous system of mice was sufficient to induce motor dysfunction, neurodegeneration, mitochondrial abnormalities and transcriptional alterations that recapitulated HD-like phenotypes. Expression of dominant-negative PPAR-delta specifically in the striatum of medium spiny neurons in mice yielded HD-like motor phenotypes, accompanied by striatal neuron loss. In mouse models of HD, pharmacologic activation of PPAR-delta using the agonist KD3010 improved motor function, reduced neurodegeneration and increased survival. PPAR-delta activation also reduced HTT-induced neurotoxicity in vitro and in medium spiny-like neurons generated from stem cells derived from individuals with HD, indicating that PPAR-delta activation may be beneficial in HD and related disorders.

Kumar, N, Richter J, Cutts J, Bush KT, Trujillo C, Nigam SK, Gaasterland T, Brafman D, Willert K.  2015.  Generation of an expandable intermediate mesoderm restricted progenitor cell line from human pluripotent stem cells. Elife. 4   10.7554/eLife.08413   AbstractWebsite

The field of tissue engineering entered a new era with the development of human pluripotent stem cells (hPSCs), which are capable of unlimited expansion whilst retaining the potential to differentiate into all mature cell populations. However, these cells harbor significant risks, including tumor formation upon transplantation. One way to mitigate this risk is to develop expandable progenitor cell populations with restricted differentiation potential. Here, we used a cellular microarray technology to identify a defined and optimized culture condition that supports the derivation and propagation of a cell population with mesodermal properties. This cell population, referred to as intermediate mesodermal progenitor (IMP) cells, is capable of unlimited expansion, lacks tumor formation potential, and, upon appropriate stimulation, readily acquires properties of a sub- population of kidney cells. Interestingly, IMP cells fail to differentiate into other mesodermally-derived tissues, including blood and heart, suggesting that these cells are restricted to an intermediate mesodermal fate.

Moya, N, Cutts J, Gaasterland T, Willert K, Brafman DA.  2014.  Endogenous WNT signaling regulates hPSC-derived neural progenitor cell heterogeneity and specifies their regional identity. Stem Cell Reports. 3:1015-1028.   10.1016/j.stemcr.2014.10.004   AbstractWebsite

Neural progenitor cells (NPCs) derived from human pluripotent stem cells (hPSCs) are a multipotent cell population that is capable of nearly indefinite expansion and subsequent differentiation into the various neuronal and supporting cell types that comprise the CNS. However, current protocols for differentiating NPCs toward neuronal lineages result in a mixture of neurons from various regions of the CNS. In this study, we determined that endogenous WNT signaling is a primary contributor to the heterogeneity observed in NPC cultures and neuronal differentiation. Furthermore, exogenous manipulation of WNT signaling during neural differentiation, through either activation or inhibition, reduces this heterogeneity in NPC cultures, thereby promoting the formation of regionally homogeneous NPC and neuronal cultures. The ability to manipulate WNT signaling to generate regionally specific NPCs and neurons will be useful for studying human neural development and will greatly enhance the translational potential of hPSCs for neural-related therapies.

Dubinsky, AN, Dastidar SG, Hsu CL, Zahra R, Djakovic SN, Duarte S, Esau CC, Spencer B, Ashe TD, Fischer KM, MacKenna DA, Sopher BL, Masliah E, Gaasterland T, Chau BN, de Almeida LP, Morrison BE, La Spada AR.  2014.  Let-7 coordinately suppresses components of the amino acid sensing pathway to repress mTORC1 and induce autophagy. Cell Metabolism. 20:626-638.   10.1016/j.cmet.2014.09.001   AbstractWebsite

Macroautophagy (hereafter autophagy) is the major pathway by which macromolecules and organelles are degraded. Autophagy is regulated by the mTOR signaling pathway-the focal point for integration of metabolic information, with mTORC1 playing a central role in balancing biosynthesis and catabolism. Of the various inputs to mTORC1, the amino acid sensing pathway is among the most potent. Based upon transcriptome analysis of neurons subjected to nutrient deprivation, we identified let-7 microRNA as capable of promoting neuronal autophagy. We found that let-7 activates autophagy by coordinately down-regulating the amino acid sensing pathway to prevent mTORC1 activation. Let-7 induced autophagy in the brain to eliminate protein aggregates, establishing its physiological relevance for in vivo autophagy modulation. Moreover, peripheral delivery of let-7 anti-miR repressed autophagy in muscle and white fat, suggesting that let-7 autophagy regulation extends beyond CNS. Hence, let-7 plays a central role in nutrient homeostasis and proteostasis regulation in higher organisms.

Allison, KA, Kaikkonen MU, Gaasterland T, Glass CK.  2014.  Vespucci: a system for building annotated databases of nascent transcripts. Nucleic Acids Research. 42:2433-2447.   10.1093/nar/gkt1237   AbstractWebsite

Global run-on sequencing (GRO-seq) is a recent addition to the series of high-throughput sequencing methods that enables new insights into transcriptional dynamics within a cell. However, GRO-sequencing presents new algorithmic challenges, as existing analysis platforms for ChIP-seq and RNA-seq do not address the unique problem of identifying transcriptional units de novo from short reads located all across the genome. Here, we present a novel algorithm for de novo transcript identification from GRO-sequencing data, along with a system that determines transcript regions, stores them in a relational database and associates them with known reference annotations. We use this method to analyze GRO-sequencing data from primary mouse macrophages and derive novel quantitative insights into the extent and characteristics of non-coding transcription in mammalian cells. In doing so, we demonstrate that Vespucci expands existing annotations for mRNAs and lincRNAs by defining the primary transcript beyond the polyadenylation site. In addition, Vespucci generates assemblies for un-annotated non-coding RNAs such as those transcribed from enhancer-like elements. Vespucci thereby provides a robust system for defining, storing and analyzing diverse classes of primary RNA transcripts that are of increasing biological interest.

Fernandez, A, Huggins IJ, Perna L, Brafman D, Lu DS, Yao SY, Gaasterland T, Carson DA, Willert K.  2014.  The WNT receptor FZD7 is required for maintenance of the pluripotent state in human embryonic stem cells. Proceedings of the National Academy of Sciences of the United States of America. 111:1409-1414.   10.1073/pnas.1323697111   AbstractWebsite

WNT signaling is involved in maintaining stem cells in an undifferentiated state; however, it is often unclear which WNTs and WNT receptors are mediating these activities. Here we examined the role of the WNT receptor FZD7 in maintaining human embryonic stem cells (hESCs) in an undifferentiated and pluripotent state. FZD7 expression is significantly elevated in undifferentiated cells relative to differentiated cell populations, and interfering with its expression or function, either by short hairpin RNA-mediated knockdown or with a fragment antigen binding (Fab) molecule directed against FZD7, disrupts the pluripotent state of hESCs. The FZD7-specific Fab blocks signaling by Wnt3a protein by downregulating FZD7 protein levels, suggesting that FZD7 transduces Wnt signals to activate Wnt/beta-catenin signaling. These results demonstrate that FZD7 encodes a regulator of the pluripotent state and that hESCs require endogenous WNT/beta-catenin signaling through FZD7 to maintain an undifferentiated phenotype.

Brafman, DA, Moya N, Allen-Soltero S, Fellner T, Robinson M, McMillen ZL, Gaasterland T, Willert K.  2013.  Analysis of SOX2-expressing cell populations derived from human pluripotent stem cells. Stem Cell Reports. 1:464-478.   10.1016/j.stemcr.2013.09.005   AbstractWebsite

SOX2 is involved in several cell and developmental processes, including maintenance of embryonic stem cells, differentiation of neural progenitor cells, and patterning of gut endoderm. To study its role in a human system, we generated a human embryonic stem cell (hESC) line harboring a reporter gene encoding GFP in the SOX2 locus. This SOX2 reporter line faithfully recapitulates expression of the SOX2 gene in undifferentiated human pluripotent stem cells (hPSCs), neural progenitor cells (NPCs), and anterior foregut endoderm (AFE). In undifferentiated hESCs, GFP expression corresponds to those cells with highest levels of expression of genes associated with the pluripotent state. In NPCs, expression of GFP can be employed to isolate cells expressing markers associated with NPC multipotency. In AFE, we used transcriptome-wide expression analysis to identify cell surface markers with elevated expression in this population, thereby facilitating isolation and purification of this hPSC-derived cell population.

Bauer, M, Benard J, Gaasterland T, Willert K, Cappellen D.  2013.  WNT5A encodes two isoforms with distinct functions in cancers. Plos One. 8   10.1371/journal.pone.0080526   AbstractWebsite

WNT5A, a member of the WNT family of secreted lipid-modified glycoproteins, is a critical regulator of a host of developmental processes, including limb formation, lung morphogenesis, intestinal elongation and mammary gland development. Altered WNT5A expression has been associated with a number of cancers. Interestingly, in certain types of cancers, such as hematological malignancies and colorectal carcinoma, WNT5A is inactivated and exerts a tumor suppressive function, while in other cancers, such as melanoma and gastric carcinoma, WNT5A is overexpressed and promotes tumor progression. The mechanism by which WNT5A achieves these distinct activities in cancers is poorly understood. Here, we provide evidence that the WNT5A gene produces two protein isoforms, WNT5A-long (WNT5A-L) and WNT5A-short (WNT5A-S). Amino-terminal sequencing and a WNT5A-L specific antibody demonstrate that the mature and secreted isoforms are distinct, with WNT5A-L carrying an additional 18 N-terminal amino acids. Biochemical analysis indicates that both purified proteins are similar with respect to their stability, hydrophobicity and WNT/beta-catenin signaling activity. Nonetheless, modulation of these two WNT5A isoforms, either through ectopic expression or knockdown, demonstrates that they exert distinct activities in cancer cell lines: while WNT5A-L inhibits proliferation of tumor cell lines, WNT5A-S promotes their growth. Finally, we show that expression of these two WNT5A isoforms is altered in breast and cervix carcinomas, as well as in the most aggressive neuroblastoma tumors. In these cancers, WNT5A-L is frequently down-regulated, whereas WNT5A-S is found overexpressed in a significant fraction of tumors. Altogether, our study provides evidence that the distinct activities of WNT5A in cancer can be attributed to the production of two WNT5A isoforms.

Pasquale, LR, Loomis SJ, Kang JH, Yaspan BL, Abdrabou W, Budenz DL, Chen TC, Delbono E, Friedman DS, Gaasterland DE, Gaasterland T, Grosskreutz CL, Lee RK, Lichter PR, Liu Y, McCarty CA, Moroi SE, Olson LM, Realini T, Rhee DJ, Schuman JS, Singh K, Vollrath D, Wollstein G, Zack DJ, Allingham RR, Pericak-Vance MA, Weinreb RN, Zhang K, Hauser MA, Richards JE, Haines JL, Wiggs JL.  2013.  CDKN2B-AS1 genotype-glaucoma feature correlations in primary open-angle glaucoma patients from the United States. American Journal of Ophthalmology. 155(2):342-353.   10.1016/j.ajo.2012.07.023  
Kandarian, B, Sethi J, Wu AA, Baker M, Yazdani N, Kym E, Sanchez A, Edsall L, Gaasterland T, Macagno E.  2012.  The medicinal leech genome encodes 21 innexin genes: different combinations are expressed by identified central neurons. Development Genes and Evolution. 222:29-44.   10.1007/s00427-011-0387-z   AbstractWebsite

Gap junctional proteins are important components of signaling pathways required for the development and ongoing functions of all animal tissues, particularly the nervous system, where they function in the intracellular and extracellular exchange of small signaling factors and ions. In animals whose genomes have been sufficiently sequenced, large families of these proteins, connexins, pannexins, and innexins, have been found, with 25 innexins in the nematode Caenorhabditis elegans Starich et al. (Cell Commun Adhes 8: 311-314, 2001) and at least 37 connexins in the zebrafish Danio rerio Cruciani and Mikalsen (Biol Chem 388: 253-264, 2009). Having recently sequenced the medicinal leech Hirudo verbana genome, we now report the presence of 21 innexin genes in this species, nine more than we had previously reported from the analysis of an EST-derived transcriptomic database Dykes and Macagno (Dev Genes Evol 216: 185-97, 2006); Macagno et al. (BMC Genomics 25: 407, 2010). Gene structure analyses show that, depending on the leech innexin gene, they can contain from 0 to 6 introns, with closely related paralogs showing the same number of introns. Phylogenetic trees comparing Hirudo to another distantly related leech species, Helobdella robusta, shows a high degree of orthology, whereas comparison to other annelids shows a relatively low level. Comparisons with other Lophotrochozoans, Ecdyzozoans and with vertebrate pannexins suggest a low number (one to two) of ancestral innexin/pannexins at the protostome/deuterostome split. Whole-mount in situ hybridization for individual genes in early embryos shows that similar to 50% of the expressed innexins are detectable in multiple tissues. Expression analyses using quantitative PCR show that similar to 70% of the Hirudo innexins are expressed in the nervous system, with most of these detected in early development. Finally, quantitative PCR analysis of several identified adult neurons detects the presence of different combinations of innexin genes, a property that may underlie the participation of these neurons in different adult coupling circuits.

Taneri, B, Asilmaz E, Gaasterland T.  2012.  Biomedical Impact of Splicing Mutations Revealed through Exome Sequencing. Molecular Medicine. 18:314-319.   10.2119/molmed.2011.00126   AbstractWebsite

Splicing is a cellular mechanism, which dictates eukaryotic gene expression by removing the noncoding introns and ligating the coding exons in the form of a messenger RNA molecule. Alternative splicing (AS) adds a major level of complexity to this mechanism and thus to the regulation of gene expression. This widespread cellular phenomenon generates multiple messenger RNA isoforms from a single gene, by utilizing alternative splice sites and promoting different exon-intron inclusions and exclusions. AS greatly increases the coding potential of eukaryotic genomes and hence contributes to the diversity of eukaryotic proteomes. Mutations that lead to disruptions of either constitutive splicing or AS cause several diseases, among which are myotonic dystrophy and cystic fibrosis. Aberrant splicing is also well established in cancer states. Identification of rare novel mutations associated with splice-site recognition, and splicing regulation in general, could provide further insight into genetic mechanisms of rare diseases. Here, disease relevance of aberrant splicing is reviewed, and the new methodological approach of starting from disease phenotype, employing exome sequencing and identifying rare mutations affecting splicing regulation is described. Exome sequencing has emerged as a reliable method for finding sequence variations associated with various disease states. To date, genetic studies using exome sequencing to find disease-causing mutations have focused on the discovery of nonsynonymous single nucleotide polymorphisms that alter amino acids or introduce early stop codons, or on the use of exome sequencing as a means to genotype known single nucleotide polymorphisms. The involvement of splicing mutations in inherited diseases has received little attention and thus likely occurs more frequently than currently estimated. Studies of exome sequencing followed by molecular and bioinformatic analyses have great potential to reveal the high impact of splicing mutations underlying human disease. Online address: doi: 10.2119/molmed.2011.00126

Van Nieuwerburgh, F, Thompson RC, Ledesma J, Deforce D, Gaasterland T, Ordoukhanian P, Head SR.  2012.  Illumina mate-paired DNA sequencing-library preparation using Cre-Lox recombination. Nucleic Acids Research. 40   10.1093/nar/gkr1000   AbstractWebsite

Standard Illumina mate-paired libraries are constructed from 3- to 5-kb DNA fragments by a blunt-end circularization. Sequencing reads that pass through the junction of the two joined ends of a 3-5-kb DNA fragment are not easy to identify and pose problems during mapping and de novo assembly. Longer read lengths increase the possibility that a read will cross the junction. To solve this problem, we developed a mate-paired protocol for use with Illumina sequencing technology that uses Cre-Lox recombination instead of blunt end circularization. In this method, a LoxP sequence is incorporated at the junction site. This sequence allows screening reads for junctions without using a reference genome. Junction reads can be trimmed or split at the junction. Moreover, the location of the LoxP sequence in the reads distinguishes mate-paired reads from spurious paired-end reads. We tested this new method by preparing and sequencing a mate-paired library with an insert size of 3 kb from Saccharomyces cerevisiae. We present an analysis of the library quality statistics and a new bio-informatics tool called DeLoxer that can be used to analyze an IlluminaCre-Lox mate-paired data set. We also demonstrate how the resulting data significantly improves a de novo assembly of the S. cerevisiae genome.

Wiggs, JL, Yaspan BL, Hauser MA, Kang JH, Allingham RR, Olson LM, Abdrabou W, Fan BJ, Wang DY, Brodeur W, Budenz DL, Caprioli J, Crenshaw A, Crooks K, Delbono E, Doheny KF, Friedman DS, Gaasterland DE, Gaasterland T, Laurie C, Lee RK, Lichter PR, Loomis S, Liu Y, Medeiros FA, McCarty C, Mirel D, Moroi SE, Musch DC, Realini A, Rozsa FW, Schuman JS, Scott K, Singh K, Stein JD, Trager EH, Vanveldhuisen P, Vollrath D, Wollstein G, Yonehama S, Zhang K, Weinreb RN, Ernst J, Kellis M, Masuda T, Zack D, Richards JE, Pericak-Vance M, Pasquale LR, Haines JL.  2012.  Common variants at 9p21 and 8q22 are associated with increased susceptibility to optic nerve degeneration in glaucoma. PLoS Genetics. 8(4):e1002654.   10.1371/journal.pgen.1002654  
Cukras, C, Gaasterland T, Lee P, Gudiseva HV, Chavali VR, Pullakhandam R, Maranhao B, Edsall L, Soares S, Reddy GB, Sieving P, Ayyagari R.  2012.  Exome analysis identified a novel mutation in the RBP4 gene in a consanguineous pedigree with retinal dystrophy and developmental abnormalities. PLoS One. 7(11):e50205.   10.1371/journal.pone.0050205  
Duncan, JL, Roorda A, Navani M, Vishweswaraiah S, Syed R, Soudry S, Ratnam K, Gudiseva HV, Lee P, Gaasterland T, Ayyagari R.  2012.  Identification of a novel mutation in the CDHR1 gene in a family with recessive retinal degeneration. Archives of Ophthalmology. 130(10):1301-1308.   10.1001/archophthalmol.2012.1906  
Wiggs, JL, Hauser MA, Abdrabou W, Allingham RR, Budenz DL, bono DE, Friedman DS, Kang JH, Gaasterland DE, Gaasterland T, Lee RK, Lichter PR, Loomis S, Liu Y, McCarty C, Medeiros FA, Moroi SE, Olson LM, Realini A, Richards JE, Rozsa FW, Schuman JS, Singh K, Stein JD, Vollrath D, Weinreb RN, Wollstein G, Yaspan BL, Yoneyama S, Zack D, Zhang K, Pericak-Vance MA, Pasquale LR, Haines JL.  2012.  The NEIGHBOR Consortium Primary Open-Angle Glaucoma Genome-wide Association Study: Rationale, Study Design, and Clinical Variables. Journal of Glaucoma. Epub ahead of print   PMC3485429  
Rost, B, Gaasterland T, Lengauer T, Linial M, Markel S, McKay BJM, Schneider R, Horton P, Kelso J.  2012.  Paving the future: finding suitable ISMB venues. Bioinformatics. Bioinformatics. 28(19):2556-2559.   PMC3463122  
Lee, PL, Gaasterland T, Barton JC.  2012.  Mild Iron Overload in an African American Man with SLC40A1 D270V. Acta Haematologica. 128:28-32.   10.1159/000337034   AbstractWebsite

We report on a 46-year-old black man who resided in Alabama with normal transferrin saturation, mild hyperferritinemia, chronic hepatitis C, and 3+ iron in hepatocytes and Kupffer cells. Exome sequencing revealed heterozygosity for SLC40A1 D270V (exon 7, c.809A -> T), a mutation previously reported only in 1 black patient with iron overload who resided in the Republic of South Africa. The present patient was also heterozygous for: heme transporter FLVCR1 novel allele P542S (exon 10, 1624C -> T); FLVCR1 T544M (rs3207090); hemopexin (HPX) R371W (rs75307540); ferritin scavenger receptor (SCARA5) R471H (rs61737287); and transferrin receptor (TFRC) G420S (rs41295879). He had no HFE, TFR2, HJV, or HAMP mutations. D270V was not detected in 19 other African Americans with iron overload who resided in Alabama. The allele frequency of SLC40A1 D270V in 258 African American adults who participated in a health appraisal clinic was 0.0019 (95% confidence interval 0-0.0057). D270V could explain 'classical' ferroportin hemochromatosis phenotypes in some African Americans. Copyright (C) 2012 S. Karger AG, Basel

Sopher, BL, Ladd PD, Pineda VV, Libby RT, Sunkin SM, Hurley JB, Thienes CP, Gaasterland T, Filippova GN, La Spada AR.  2011.  CTCF Regulates Ataxin-7 Expression through Promotion of a Convergently Transcribed, Antisense Noncoding RNA. Neuron. 70:1071-1084.   10.1016/j.neuron.2011.05.027   AbstractWebsite

Spinocerebellar ataxia type 7 (SCA7) is a neurodegenerative disorder caused by CAG/polyglutamine repeat expansions in the ataxin-7 gene. Ataxin-7 is a component of two different transcription coactivator complexes, and recent work indicates that disease protein normal function is altered in polyglutamine neurodegeneration. Given this, we studied how ataxin-7 gene expression is regulated. The ataxin-7 repeat and translation start site are flanked by binding sites for CTCF, a highly conserved multifunctional transcription regulator. When we analyzed this region, we discovered an adjacent alternative promoter and a convergently transcribed antisense noncoding RNA, SCAANT1. To understand how CTCF regulates ataxin-7 gene expression, we introduced ataxin-7 mini-genes into mice, and found that CTCF is required for SCAANT1 expression. Loss of SCAANT1 derepressed ataxin-7 sense transcription in a cis-dependent fashion and was accompanied by chromatin remodeling. Discovery of this pathway underscores the importance of altered epigenetic regulation for disease pathology at repeat loci exhibiting bidirectional transcription.

Norden-Krichmar, TM, Allen AE, Gaasterland T, Hildebrand M.  2011.  Characterization of the Small RNA Transcriptome of the Diatom, Thalassiosira pseudonana. Plos One. 6   10.1371/journal.pone.0022870   AbstractWebsite

This study presents the first characterization of endogenous small RNAs in a diatom, Thalassiosira pseudonana. Small RNAs act as transcriptional and translational regulators, controlling specific target genes involved in various cellular functions. Diatoms are unicellular photosynthetic organisms that play major roles in environmental processes, such as food webs and global carbon fixation. Small RNA cDNA libraries were constructed for exponentially growing T. pseudonana, and then subjected to highly parallel pyrosequencing (454) and sequencing-by-ligation (Applied Biosystems SOLiD). From the computational analysis of approximately 300,000 sequences in the 454 library and over 17 million sequences in the SOLiD libraries, there exists evidence of a core set of small RNA genes including: novel microRNAs, repeat-associated short interfering RNAs, and endogenous short interfering RNAs. The diatom genome contains elements similar to plant small RNA systems, such as the RNAi machinery, a high percentage of short interfering RNAs originating from protein-coding and repetitive regions of the genome, and putative binding sites of the small RNAs occurring primarily in the coding section of the predicted targets. The characterization of the small RNA transcriptome of T. pseudonana establishes the possibility of a wide range of gene regulatory mechanisms in diatoms.

Bruand, J, Sistla S, Meriaux C, Dorrestein PC, Gaasterland T, Ghassemian M, Wisztorski M, Fournier I, Salzet M, Macagno E, Bafna V.  2011.  Automated Querying and Identification of Novel Peptides using MALDI Mass Spectrometric Imaging. Journal of Proteome Research. 10:1915-1928.   10.1021/pr101159e   AbstractWebsite

MSI is a molecular imaging technique that allows for the generation of topographic 2D maps for various endogenous and some exogenous molecules without prior specification of the molecule. In this paper, we start with the premise that a region of interest (ROI) is given to us based on preselected morphological criteria. Given an ROT, we develop a pipeline, first to determine mass values with distinct expression signatures, localized to the ROI, and second to identify the peptides corresponding to these mass values. To identify spatially differentiated masses, we implement a statistic that allows us to estimate, for each spectral peak, the probability that it is over- or under-expressed within the ROI versus outside. To identify peptides corresponding to these masses, we apply LC-MS/MS to fragment endogenous (nonprotease digested) peptides. A novel pipeline based on constructing sequence tags de novo from both original and decharged spectra and a subsequent database search is used to identify peptides. As the MSI signal and the identified peptide are only related by a single mass value, we isolate the corresponding transcript and perform a second validation via in situ hybridization of the transcript. We tested our approach, MSI-Query, on a number of ROIs in the medicinal leech, Hirudo medicinalis, including the central nervous system (CNS). The Hirudo CNS is capable of regenerating itself after injury, thus forming an important model system for neuropeptide identification. The pipeline helps identify a number of novel peptides. Specifically, we identify a gene that we name HmIF4, which is a member of the intermediate filament family involved in neural development and a second novel, uncharacterized peptide. A third peptide, derived from the histone H2B, is also identified, in agreement with the previously suggested role of histone H2B in axon targeting.

Meriaux, C, Arafah K, Tasiemski A, Wisztorski M, Bruand J, Boidin-Wichlacz C, Desmons A, Debois D, Laprevote O, Brunelle A, Gaasterland T, Macagno E, Fournier I, Salzet M.  2011.  Multiple Changes in Peptide and Lipid Expression Associated with Regeneration in the Nervous System of the Medicinal Leech. Plos One. 6   10.1371/journal.pone.0018359   AbstractWebsite

BACKGROUND: The adult medicinal leech central nervous system (CNS) is capable of regenerating specific synaptic circuitry after a mechanical lesion, displaying evidence of anatomical repair within a few days and functional recovery within a few weeks. In the present work, spatiotemporal changes in molecular distributions during this phenomenon are explored. Moreover, the hypothesis that neural regeneration involves some molecular factors initially employed during embryonic neural development is tested. RESULTS: Imaging mass spectrometry coupled to peptidomic and lipidomic methodologies allowed the selection of molecules whose spatiotemporal pattern of expression was of potential interest. The identification of peptides was aided by comparing MS/MS spectra obtained for the peptidome extracted from embryonic and adult tissues to leech transcriptome and genome databases. Through the parallel use of a classical lipidomic approach and secondary ion mass spectrometry, specific lipids, including cannabinoids, gangliosides and several other types, were detected in adult ganglia following mechanical damage to connected nerves. These observations motivated a search for possible effects of cannabinoids on neurite outgrowth. Exposing nervous tissues to Transient Receptor Potential Vanilloid (TRPV) receptor agonists resulted in enhanced neurite outgrowth from a cut nerve, while exposure to antagonists blocked such outgrowth. CONCLUSION: The experiments on the regenerating adult leech CNS reported here provide direct evidence of increased titers of proteins that are thought to play important roles in early stages of neural development. Our data further suggest that endocannabinoids also play key roles in CNS regeneration, mediated through the activation of leech TRPVs, as a thorough search of leech genome databases failed to reveal any leech orthologs of the mammalian cannabinoid receptors but revealed putative TRPVs. In sum, our observations identify a number of lipids and proteins that may contribute to different aspects of the complex phenomenon of leech nerve regeneration, establishing an important base for future functional assays.

Junier, P, Junier T, Podell S, Sims DR, Detter JC, Lykidis A, Han CS, Wigginton NS, Gaasterland T, Bernier-Latmani R.  2010.  The genome of the Gram-positive metal- and sulfate-reducing bacterium Desulfotomaculum reducens strain MI-1. Environmental Microbiology. 12:2738-2754.   10.1111/j.1462-2920.2010.02242.x   AbstractWebsite

P>Spore-forming, Gram-positive sulfate-reducing bacteria (SRB) represent a group of SRB that dominates the deep subsurface as well as niches in which resistance to oxygen and dessication is an advantage. Desulfotomaculum reducens strain MI-1 is one of the few cultured representatives of that group with a complete genome sequence available. The metabolic versatility of this organism is reflected in the presence of genes encoding for the oxidation of various electron donors, including three- and four-carbon fatty acids and alcohols. Synteny in genes involved in sulfate reduction across all four sequenced Gram-positive SRB suggests a distinct sulfate-reduction mechanism for this group of bacteria. Based on the genomic information obtained for sulfate reduction in D. reducens, the transfer of electrons to the sulfite and APS reductases is proposed to take place via the quinone pool and heterodisulfide reductases respectively. In addition, both H(2)-evolving and H(2)-consuming cytoplasmic hydrogenases were identified in the genome, pointing to potential cytoplasmic H(2) cycling in the bacterium. The mechanism of metal reduction remains unknown.

Macagno, ER, Gaasterland T, Edsall L, Bafna V, Soares MB, Scheetz T, Casavant T, Da Silva C, Wincker P, Tasiemski A, Salzet M.  2010.  Construction of a medicinal leech transcriptome database and its application to the identification of leech homologs of neural and innate immune genes. Bmc Genomics. 11   10.1186/1471-2164-11-407   AbstractWebsite

Background: The medicinal leech, Hirudo medicinalis, is an important model system for the study of nervous system structure, function, development, regeneration and repair. It is also a unique species in being presently approved for use in medical procedures, such as clearing of pooled blood following certain surgical procedures. It is a current, and potentially also future, source of medically useful molecular factors, such as anticoagulants and antibacterial peptides, which may have evolved as a result of its parasitizing large mammals, including humans. Despite the broad focus of research on this system, little has been done at the genomic or transcriptomic levels and there is a paucity of openly available sequence data. To begin to address this problem, we constructed whole embryo and adult central nervous system (CNS) EST libraries and created a clustered sequence database of the Hirudo transcriptome that is available to the scientific community. Results: A total of similar to 133,000 EST clones from two directionally-cloned cDNA libraries, one constructed from mRNA derived from whole embryos at several developmental stages and the other from adult CNS cords, were sequenced in one or both directions by three different groups: Genoscope (French National Sequencing Center), the University of Iowa Sequencing Facility and the DOE Joint Genome Institute. These were assembled using the phrap software package into 31,232 unique contigs and singletons, with an average length of 827 nt. The assembled transcripts were then translated in all six frames and compared to proteins in NCBI's non-redundant (NR) and to the Gene Ontology (GO) protein sequence databases, resulting in 15,565 matches to 11,236 proteins in NR and 13,935 matches to 8,073 proteins in GO. Searching the database for transcripts of genes homologous to those thought to be involved in the innate immune responses of vertebrates and other invertebrates yielded a set of nearly one hundred evolutionarily conserved sequences, representing all known pathways involved in these important functions. Conclusions: The sequences obtained for Hirudo transcripts represent the first major database of genes expressed in this important model system. Comparison of translated open reading frames (ORFs) with the other openly available leech datasets, the genome and transcriptome of Helobdella robusta, shows an average identity at the amino acid level of 58% in matched sequences. Interestingly, comparison with other available Lophotrochozoans shows similar high levels of amino acid identity, where sequences match, for example, 64% with Capitella capitata (a polychaete) and 56% with Aplysia californica (a mollusk), as well as 58% with Schistosoma mansoni (a platyhelminth). Phylogenetic comparisons of putative Hirudo innate immune response genes present within the Hirudo transcriptome database herein described show a strong resemblance to the corresponding mammalian genes, indicating that this important physiological response may have older origins than what has been previously proposed.