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Repertoire Sequencing

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https://www.readbyqxmd.com/read/27923045/tumor-evolution-in-two-patients-with-basal-like-breast-cancer-a-retrospective-genomics-study-of-multiple-metastases
#1
Katherine A Hoadley, Marni B Siegel, Krishna L Kanchi, Christopher A Miller, Li Ding, Wei Zhao, Xiaping He, Joel S Parker, Michael C Wendl, Robert S Fulton, Ryan T Demeter, Richard K Wilson, Lisa A Carey, Charles M Perou, Elaine R Mardis
BACKGROUND: Metastasis is the main cause of cancer patient deaths and remains a poorly characterized process. It is still unclear when in tumor progression the ability to metastasize arises and whether this ability is inherent to the primary tumor or is acquired well after primary tumor formation. Next-generation sequencing and analytical methods to define clonal heterogeneity provide a means for identifying genetic events and the temporal relationships between these events in the primary and metastatic tumors within an individual...
December 2016: PLoS Medicine
https://www.readbyqxmd.com/read/27904140/restrictions-in-the-t-cell-repertoire-of-chronic-lymphocytic-leukemia-high-throughput-immunoprofiling-supports-selection-by-shared-antigenic-elements
#2
A Vardi, E Vlachonikola, M Karypidou, E Stalika, V Bikos, K Gemenetzi, C Maramis, A Siorenta, A Anagnostopoulos, S Pospisilova, N Maglaveras, I Chouvarda, K Stamatopoulos, A Hadzidimitriou
Immunoglobulin (IG) gene repertoire restrictions strongly support antigen selection in the pathogenesis of chronic lymphocytic leukemia (CLL). Given the emerging multifarious interactions between CLL and bystander T cells, we sought to determine whether antigen(s) are also selecting T cells in CLL. We performed a large-scale, next-generation sequencing (NGS) study of the T-cell repertoire, focusing on major stereotyped subsets representing CLL subgroups with undisputed antigenic drive, but also included patients carrying non-subset IG rearrangements to seek for T-cell immunogenetic signatures ubiquitous in CLL...
December 1, 2016: Leukemia: Official Journal of the Leukemia Society of America, Leukemia Research Fund, U.K
https://www.readbyqxmd.com/read/27901108/survey-of-the-green-picoalga-bathycoccus-genomes-in-the-global-ocean
#3
Thomas Vannier, Jade Leconte, Yoann Seeleuthner, Samuel Mondy, Eric Pelletier, Jean-Marc Aury, Colomban de Vargas, Michael Sieracki, Daniele Iudicone, Daniel Vaulot, Patrick Wincker, Olivier Jaillon
Bathycoccus is a cosmopolitan green micro-alga belonging to the Mamiellophyceae, a class of picophytoplankton that contains important contributors to oceanic primary production. A single species of Bathycoccus has been described while the existence of two ecotypes has been proposed based on metagenomic data. A genome is available for one strain corresponding to the described phenotype. We report a second genome assembly obtained by a single cell genomics approach corresponding to the second ecotype. The two Bathycoccus genomes are divergent enough to be unambiguously distinguishable in whole DNA metagenomic data although they possess identical sequence of the 18S rRNA gene including in the V9 region...
November 30, 2016: Scientific Reports
https://www.readbyqxmd.com/read/27896960/on-the-power-and-limits-of-sequence-similarity-based-clustering-of-proteins-into-families
#4
Christian Wiwie, Richard Röttger
Over the last decades, we have observed an ongoing tremendous growth of available sequencing data fueled by the advancements in wet-lab technology. The sequencing information is only the beginning of the actual understanding of how organisms survive and prosper. It is, for instance, equally important to also unravel the proteomic repertoire of an organism. A classical computational approach for detecting protein families is a sequence-based similarity calculation coupled with a subsequent cluster analysis. In this work we have intensively analyzed various clustering tools on a large scale...
2016: Pacific Symposium on Biocomputing
https://www.readbyqxmd.com/read/27896747/studying-antibody-repertoires-with-next-generation-sequencing
#5
William D Lees, Adrian J Shepherd
Next-generation sequencing is making it possible to study the antibody repertoire of an organism in unprecedented detail, and, by so doing, to characterize its behavior in the response to infection and in pathological conditions such as autoimmunity and cancer. The polymorphic nature of the repertoire poses unique challenges that rule out the use of many commonly used NGS methods and require tradeoffs to be made when considering experimental design.We outline the main contexts in which antibody repertoire analysis has been used, and summarize the key tools that are available...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896721/the-classification-of-protein-domains
#6
Natalie Dawson, Ian Sillitoe, Russell L Marsden, Christine A Orengo
The significant expansion in protein sequence and structure data that we are now witnessing brings with it a pressing need to bring order to the protein world. Such order enables us to gain insights into the evolution of proteins, their function and the extent to which the functional repertoire can vary across the three kingdoms of life. This has lead to the creation of a wide range of protein family classifications that aim to group proteins based upon their evolutionary relationships.In this chapter we discuss the approaches and methods that are frequently used in the classification of proteins, with a specific emphasis on the classification of protein domains...
2017: Methods in Molecular Biology
https://www.readbyqxmd.com/read/27896028/the-scavenger-receptor-repertoire-in-six-cnidarian-species-and-its-putative-role-in-cnidarian-dinoflagellate-symbiosis
#7
Emilie F Neubauer, Angela Z Poole, Virginia M Weis, Simon K Davy
Many cnidarians engage in a mutualism with endosymbiotic photosynthetic dinoflagellates that forms the basis of the coral reef ecosystem. Interpartner interaction and regulation includes involvement of the host innate immune system. Basal metazoans, including cnidarians have diverse and complex innate immune repertoires that are just beginning to be described. Scavenger receptors (SR) are a diverse superfamily of innate immunity genes that recognize a broad array of microbial ligands and participate in phagocytosis of invading microbes...
2016: PeerJ
https://www.readbyqxmd.com/read/27895807/cpas-based-sequencing-on-the-bgiseq-500-to-explore-small-non-coding-rnas
#8
Tobias Fehlmann, Stefanie Reinheimer, Chunyu Geng, Xiaoshan Su, Snezana Drmanac, Andrei Alexeev, Chunyan Zhang, Christina Backes, Nicole Ludwig, Martin Hart, Dan An, Zhenzhen Zhu, Chongjun Xu, Ao Chen, Ming Ni, Jian Liu, Yuxiang Li, Matthew Poulter, Yongping Li, Cord Stähler, Radoje Drmanac, Xun Xu, Eckart Meese, Andreas Keller
BACKGROUND: We present the first sequencing data using the combinatorial probe-anchor synthesis (cPAS)-based BGISEQ-500 sequencer. Applying cPAS, we investigated the repertoire of human small non-coding RNAs and compared it to other techniques. RESULTS: Starting with repeated measurements of different specimens including solid tissues (brain and heart) and blood, we generated a median of 30.1 million reads per sample. 24.1 million mapped to the human genome and 23...
2016: Clinical Epigenetics
https://www.readbyqxmd.com/read/27894837/cd4-virtual-memory-antigen-inexperienced-t-cells-reside-in-the-na%C3%A3-ve-regulatory-and-memory-t-cell-compartments-at-similar-frequencies-implications-for-autoimmunity
#9
Alina I Marusina, Yoko Ono, Alexander A Merleev, Michiko Shimoda, Hiromi Ogawa, Elizabeth A Wang, Kayo Kondo, Laura Olney, Guillaume Luxardi, Yoshinori Miyamura, Tilahun D Yilma, Itzel Bustos Villalobos, Jennifer W Bergstrom, Daniel G Kronenberg, Athena M Soulika, Iannis E Adamopoulos, Emanual Maverakis
It is widely accepted that central and effector memory CD4(+) T cells originate from naïve T cells after they have encountered their cognate antigen in the setting of appropriate co-stimulation. However, if this were true the diversity of T cell receptor (TCR) sequences within the naïve T cell compartment should be far greater than that of the memory T cell compartment, which is not supported by TCR sequencing data. Here we demonstrate that aged mice with far fewer naïve T cells, respond to the model antigen, hen eggwhite lysozyme (HEL), by utilizing the same TCR sequence as their younger counterparts...
November 25, 2016: Journal of Autoimmunity
https://www.readbyqxmd.com/read/27893816/mir-34-modulates-innate-immunity-and-ecdysone-signaling-in-drosophila
#10
Xiao-Peng Xiong, Krishna Kurthkoti, Kung-Yen Chang, Jian-Liang Li, Xingjie Ren, Jian-Quan Ni, Tariq M Rana, Rui Zhou
microRNAs are endogenous small regulatory RNAs that modulate myriad biological processes by repressing target gene expression in a sequence-specific manner. Here we show that the conserved miRNA miR-34 regulates innate immunity and ecdysone signaling in Drosophila. miR-34 over-expression activates antibacterial innate immunity signaling both in cultured cells and in vivo, and flies over-expressing miR-34 display improved survival and pathogen clearance upon Gram-negative bacterial infection; whereas miR-34 knockout animals are defective in antibacterial defense...
November 2016: PLoS Pathogens
https://www.readbyqxmd.com/read/27890785/genomic-characterization-of-dysplastic-nevi-unveils-implications-for-diagnosis-of-melanoma
#11
Rachel D Melamed, Iraz T Aydin, Geena Susan Rajan, Robert Phelps, David N Silvers, Kevin J Emmett, Georg Brunner, Raul Rabadan, Julide Tok Celebi
A well-defined risk factor and precursor for cutaneous melanoma is the dysplastic nevus. These benign tumors represent clonal hyperproliferation of melanocytes that are in a senescent-like state, but with occasional malignant transformation events. To portray the mutational repertoire of dysplastic nevi in patients with the dysplastic nevus syndrome, and to determine the discriminatory profiles of melanocytic nevi (including dysplastic nevi) from melanoma, we sequenced exomes of melanocytic nevi including dysplastic nevi (n = 19), followed by a targeted gene panel (785 genes) characterization of melanocytic nevi (n = 46) and primary melanomas (n = 42)...
November 24, 2016: Journal of Investigative Dermatology
https://www.readbyqxmd.com/read/27882350/plasma-vesicle-mirnas-for-therapy-response-monitoring-in-hodgkin-lymphoma-patients
#12
Monique A J van Eijndhoven, Josée M Zijlstra, Nils J Groenewegen, Esther E E Drees, Stuart van Niele, S Rubina Baglio, Danijela Koppers-Lalic, Hans van der Voorn, Sten F W M Libregts, Marca H M Wauben, Renee X de Menezes, Jan R T van Weering, Rienk Nieuwland, Lydia Visser, Anke van den Berg, Daphne de Jong, D Michiel Pegtel
BACKGROUND. Cell-free circulating nucleic acids, including 22-nt microRNAs (miRNAs), represent noninvasive biomarkers for treatment response monitoring of cancer patients. While the majority of plasma miRNA is bound to proteins, a smaller, less well-characterized pool is associated with extracellular vesicles (EVs). Here, we addressed whether EV-associated miRNAs reflect metabolic disease in classical Hodgkin lymphoma (cHL) patients. METHODS. With standardized size-exclusion chromatography (SEC), we isolated EV-associated extracellular RNA (exRNA) fractions and protein-bound miRNA from plasma of cHL patients and healthy subjects...
November 17, 2016: JCI Insight
https://www.readbyqxmd.com/read/27880974/deep-sequencing-of-the-tcrb-repertoire-of-human-foxp3-and-foxp3-t-cells-suggests-that-they-are-completely-distinct-and-non-overlapping
#13
Amit Golding, Samuel Darko, William H Wylie, Daniel C Douek, Ethan M Shevach
Maintenance of peripheral tolerance requires a balance between auto-reactive conventional T cells (Tconv) and thymically-derived Foxp3(+) regulatory T cells (tTregs). Considerable controversy exists regarding the similarities/differences in TCR repertoires expressed by Tconv and tTregs. We generated highly purified populations of human adult and cord blood Tconv and tTregs based on the differential expression of CD25 and CD127. The purity of the sorted populations was validated by intracellular staining for Foxp3 and Helios...
November 23, 2016: Clinical and Experimental Immunology
https://www.readbyqxmd.com/read/27880868/origin-and-evolution-of-the-metazoan-non-coding-regulatory-genome
#14
REVIEW
Federico Gaiti, Andrew D Calcino, Miloš Tanurdžić, Bernard M Degnan
Animals rely on genomic regulatory systems to direct the dynamic spatiotemporal and cell-type specific gene expression that is essential for the development and maintenance of a multicellular lifestyle. Although it is widely appreciated that these systems ultimately evolved from genomic regulatory mechanisms present in single-celled stem metazoans, it remains unclear how this occurred. Here, we focus on the contribution of the non-coding portion of the genome to the evolution of animal gene regulation, specifically on recent insights from non-bilaterian metazoan lineages, and unicellular and colonial holozoan sister taxa...
November 20, 2016: Developmental Biology
https://www.readbyqxmd.com/read/27878834/characterization-of-mirnas-involved-in-response-to-poly-i-c-in-porcine-airway-epithelial-cells
#15
L Wang, J K Wang, L X Han, J S Zhuo, X Du, D Liu, X Q Yang
MicroRNAs (miRNA) have been implicated in a variety of pathological conditions including infectious diseases. Knowledge of the miRNAs affected by poly(I:C), a synthetic analog of viral double-stranded RNA, in porcine airway epithelial cells (PAECs) contributes to understanding the mechanisms of swine viral respiratory diseases, which bring enormous economic loss worldwide every year. In this study, we used high throughput sequencing to profile miRNA expression in PAECs treated with poly(I:C) as compared to the untreated control...
November 22, 2016: Animal Genetics
https://www.readbyqxmd.com/read/27878651/messages-on-small-rna-duplexes-in-plants
#16
Taichiro Iki
Small RNA-mediated gene silencing encompasses diverse developmental events, stress responses, defense against pathogens, and maintenance of genome integrity. Extensive studies in model organisms have unveiled the molecular mechanisms underpinning the RNA silencing phenomena, and the accumulating knowledge have characterized the intricate pathways and the repertoire of proteins responsible for the actions of small RNAs characterized as microRNAs (miRNAs) or small interfering RNAs (siRNAs). Although the single-stranded, matured guide small RNAs direct the effector ribonucleoprotein complexes to induce gene silencing in sequence-specific manner, the double-stranded intermediate, the small RNA duplexes, which are processed as nascent products of the RNase III enzyme activities, act as key to determine the downstream molecular pathways and the fate of small RNAs...
November 23, 2016: Journal of Plant Research
https://www.readbyqxmd.com/read/27875982/comparative-genomics-to-explore-phylogenetic-relationship-cryptic-sexual-potential-and-host-specificity-of-rhynchosporium-species-on-grasses
#17
Daniel Penselin, Martin Münsterkötter, Susanne Kirsten, Marius Felder, Stefan Taudien, Matthias Platzer, Kevin Ashelford, Konrad H Paskiewicz, Richard J Harrison, David J Hughes, Thomas Wolf, Ekaterina Shelest, Jenny Graap, Jan Hoffmann, Claudia Wenzel, Nadine Wöltje, Kevin M King, Bruce D L Fitt, Ulrich Güldener, Anna Avrova, Wolfgang Knogge
BACKGROUND: The Rhynchosporium species complex consists of hemibiotrophic fungal pathogens specialized to different sweet grass species including the cereal crops barley and rye. A sexual stage has not been described, but several lines of evidence suggest the occurrence of sexual reproduction. Therefore, a comparative genomics approach was carried out to disclose the evolutionary relationship of the species and to identify genes demonstrating the potential for a sexual cycle. Furthermore, due to the evolutionary very young age of the five species currently known, this genus appears to be well-suited to address the question at the molecular level of how pathogenic fungi adapt to their hosts...
November 22, 2016: BMC Genomics
https://www.readbyqxmd.com/read/27871261/quantitative-characterization-of-t-cell-repertoire-and-biomarkers-in-kidney-transplant-rejection
#18
Houda Alachkar, Martin Mutonga, Taigo Kato, Sowjanya Kalluri, Yoichi Kakuta, Motohide Uemura, Ryoichi Imamura, Norio Nonomura, Vikas Vujjini, Sami Alasfar, Hamid Rabb, Yusuke Nakamura, Nada Alachkar
BACKGROUND: T-cell-mediated rejection (TCMR) remains a major cause of kidney allograft failure. The characterization of T-cell repertoire in different immunological disorders has emerged recently as a novel tool with significant implications. We herein sought to characterize T-cell repertoire using next generation sequencing to diagnose TCMR. METHODS: In this prospective study, we analyzed samples from 50 kidney transplant recipients. We collected blood and kidney transplant biopsy samples at sequential time points before and post transplant...
November 21, 2016: BMC Nephrology
https://www.readbyqxmd.com/read/27871145/meta-omic-analyses-of-baltic-sea-cyanobacteria-diversity-community-structure-and-salt-acclimation
#19
Narin Celepli, John Sundh, Martin Ekman, Chris L Dupont, Shibu Yooseph, Birgitta Bergman, Karolina Ininbergs
Cyanobacteria are important phytoplankton in the Baltic Sea, an estuarine-like environment with pronounced north to south gradient in salinity and nutrient concentrations. Here we present a metagenomic and -transcriptomic survey, with subsequent analyses targeting the genetic identity, phylogenetic diversity, and spatial distribution of Baltic Sea cyanobacteria. The cyanobacterial community constituted close to 12% of the microbial population sampled during a pre-bloom period (June-July 2009). The community was dominated by unicellular picocyanobacteria, specifically a few highly abundant taxa (Synechococcus and Cyanobium) with a long tail of low abundance representatives, and local peaks of bloom-forming heterocystous taxa...
November 21, 2016: Environmental Microbiology
https://www.readbyqxmd.com/read/27869234/autoimmune-susceptibility-imposed-by-public-tcr%C3%AE-chains
#20
Yunqian Zhao, Phuong Nguyen, Peter Vogel, Bofeng Li, Lindsay L Jones, Terrence L Geiger
Although the TCR repertoire is highly diverse, a small fraction of TCR chains, referred to as public, preferentially form and are shared by most individuals. Prior studies indicated that public TCRβ may be preferentially deployed in autoimmunity. We hypothesized that if these TCRβ modulate the likelihood of a TCRαβ heterodimer productively engaging autoantigen, because they are widely present in the population and often high frequency within individual repertoires, they could also broadly influence repertoire responsiveness to specific autoantigens...
November 21, 2016: Scientific Reports
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