NGI offers spatial transcriptomics through the 10X Genomics Visium method, a technique recently nominated as Method of the Year by Nature Methods. The technology combines histology with unbiased transcriptomics in a spatial context.
The Illumina NovaSeq 6000 system is the largest of the Illumina sequencing instruments, able to run two flow cells independently of each other and generate massive sequencing depth at competitive prices.
Transcriptome profiling of the interconnection of pathways involved in malignant transformation and response to hypoxia.
F Danielsson, E Fasterius, D Sullivan, L Hases, K Sanli, C Zhang, A Mardinoglu, C Al-Khalili, M Huss, M Uhlén, C Williams, E Lundberg
Oncotarget, 9 (28) 1949-2553 (2018)
In tumor tissues, hypoxia is a commonly observed feature resulting from rapidly proliferating cancer cells outgrowing their surrounding vasculature network. Transformed cancer cells are known to exhibit phenotypic alterations, enabling continuous proliferation despite a limited oxygen supply. The four-step isogenic BJ cell model enables studies of defined steps of tumorigenesis: the normal, immortalized, transformed, and metastasizing stages. By transcriptome profiling under atmospheric and moderate hypoxic (3% O
Genomic Analyses of Pre-European Conquest Human Remains from the Canary Islands Reveal Close Affinity to Modern North Africans.
R Rodríguez-Varela, T Günther, M Krzewińska, J Storå, TH Gillingwater, M MacCallum, JL Arsuaga, K Dobney, C Valdiosera, M Jakobsson, A Götherström, L Girdland-Flink
Curr. Biol., 27 (21) 1879-0445 (2017)
The origins and genetic affinity of the aboriginal inhabitants of the Canary Islands, commonly known as Guanches, are poorly understood. Though radiocarbon dates on archaeological remains such as charcoal, seeds, and domestic animal bones suggest that people have inhabited the islands since the 5th century BCE [1-3], it remains unclear how many times, and by whom, the islands were first settled [4, 5]. Previously published ancient DNA analyses of uniparental genetic markers have shown that the Guanches carried common North African Y chromosome markers (E-M81, E-M78, and J-M267) and mitochondrial lineages such as U6b, in addition to common Eurasian haplogroups [6-8]. These results are in agreement with some linguistic, archaeological, and anthropological data indicating an origin from a North African Berber-like population [1, 4, 9]. However, to date there are no published Guanche autosomal genomes to help elucidate and directly test this hypothesis. To resolve this, we generated the first genome-wide sequence data and mitochondrial genomes from eleven archaeological Guanche individuals originating from Gran Canaria and Tenerife. Five of the individuals (directly radiocarbon dated to a time transect spanning the 7th-11th centuries CE) yielded sufficient autosomal genome coverage (0.21× to 3.93×) for population genomic analysis. Our results show that the Guanches were genetically similar over time and that they display the greatest genetic affinity to extant Northwest Africans, strongly supporting the hypothesis of a Berber-like origin. We also estimate that the Guanches have contributed 16%-31% autosomal ancestry to modern Canary Islanders, here represented by two individuals from Gran Canaria.
Gene-educational attainment interactions in a multi-ancestry genome-wide meta-analysis identify novel blood pressure loci.
L de Las Fuentes, YJ Sung, R Noordam, T Winkler, MF Feitosa, K Schwander, AR Bentley, MR Brown, X Guo, A Manning, DI Chasman, H Aschard, TM Bartz, LF Bielak, A Campbell, C Cheng, R Dorajoo, FP Hartwig, ARVR Horimoto, C Li, R Li-Gao, Y Liu, J Marten, SK Musani, I Ntalla, T Rankinen, M Richard, X Sim, AV Smith, SM Tajuddin, BO Tayo, D Vojinovic, HR Warren, D Xuan, M Alver, M Boissel, J Chai, X Chen, K Christensen, J Divers, E Evangelou, C Gao, G Girotto, SE Harris, M He, F Hsu, B Kühnel, F Laguzzi, X Li, L Lyytikäinen, IM Nolte, A Poveda, R Rauramaa, M Riaz, R Rueedi, X Shu, H Snieder, T Sofer, F Takeuchi, N Verweij, EB Ware, S Weiss, LR Yanek, N Amin, DE Arking, DK Arnett, S Bergmann, E Boerwinkle, JA Brody, U Broeckel, M Brumat, G Burke, CP Cabrera, M Canouil, ML Chee, YI Chen, M Cocca, J Connell, HJ de Silva, PS de Vries, G Eiriksdottir, JD Faul, V Fisher, T Forrester, EF Fox, Y Friedlander, H Gao, B Gigante, F Giulianini, CC Gu, D Gu, TB Harris, J He, S Heikkinen, C Heng, S Hunt, MA Ikram, MR Irvin, M Kähönen, M Kavousi, CC Khor, TO Kilpeläinen, W Koh, P Komulainen, AT Kraja, JE Krieger, CD Langefeld, Y Li, J Liang, DCM Liewald, C Liu, J Liu, KK Lohman, R Mägi, CA McKenzie, T Meitinger, A Metspalu, Y Milaneschi, L Milani, DO Mook-Kanamori, MA Nalls, CP Nelson, JM Norris, J O'Connell, A Ogunniyi, S Padmanabhan, ND Palmer, NL Pedersen, T Perls, A Peters, A Petersmann, PA Peyser, O Polasek, DJ Porteous, LJ Raffel, TK Rice, JI Rotter, I Rudan, O Rueda-Ochoa, C Sabanayagam, BL Salako, PJ Schreiner, JM Shikany, SS Sidney, M Sims, CM Sitlani, JA Smith, JM Starr, K Strauch, MA Swertz, A Teumer, YC Tham, AG Uitterlinden, D Vaidya, MY van der Ende, M Waldenberger, L Wang, Y Wang, W Wei, DR Weir, W Wen, J Yao, B Yu, C Yu, J Yuan, W Zhao, AB Zonderman, DM Becker, DW Bowden, IJ Deary, M Dörr, T Esko, BI Freedman, P Froguel, P Gasparini, C Gieger, JB Jonas, CM Kammerer, N Kato, TA Lakka, K Leander, T Lehtimäki, Lifelines Cohort Study, PKE Magnusson, P Marques-Vidal, BWJH Penninx, NJ Samani, P van der Harst, LE Wagenknecht, T Wu, W Zheng, X Zhu, C Bouchard, RS Cooper, A Correa, MK Evans, V Gudnason, C Hayward, BL Horta, TN Kelly, SB Kritchevsky, D Levy, WR Palmas, AC Pereira, MM Province, BM Psaty, PM Ridker, CN Rotimi, ES Tai, RM van Dam, CM van Duijn, TY Wong, K Rice, WJ Gauderman, AC Morrison, KE North, SLR Kardia, MJ Caulfield, P Elliott, PB Munroe, PW Franks, DC Rao, M Fornage
Mol. Psychiatry, 26 (6) 1476-5578 (2021)
Educational attainment is widely used as a surrogate for socioeconomic status (SES). Low SES is a risk factor for hypertension and high blood pressure (BP). To identify novel BP loci, we performed multi-ancestry meta-analyses accounting for gene-educational attainment interactions using two variables, "Some College" (yes/no) and "Graduated College" (yes/no). Interactions were evaluated using both a 1 degree of freedom (DF) interaction term and a 2DF joint test of genetic and interaction effects. Analyses were performed for systolic BP, diastolic BP, mean arterial pressure, and pulse pressure. We pursued genome-wide interrogation in Stage 1 studies (N = 117 438) and follow-up on promising variants in Stage 2 studies (N = 293 787) in five ancestry groups. Through combined meta-analyses of Stages 1 and 2, we identified 84 known and 18 novel BP loci at genome-wide significance level (P < 5 × 10-8). Two novel loci were identified based on the 1DF test of interaction with educational attainment, while the remaining 16 loci were identified through the 2DF joint test of genetic and interaction effects. Ten novel loci were identified in individuals of African ancestry. Several novel loci show strong biological plausibility since they involve physiologic systems implicated in BP regulation. They include genes involved in the central nervous system-adrenal signaling axis (ZDHHC17, CADPS, PIK3C2G), vascular structure and function (GNB3, CDON), and renal function (HAS2 and HAS2-AS1, SLIT3). Collectively, these findings suggest a role of educational attainment or SES in further dissection of the genetic architecture of BP.
Freshwater Chlorobia Exhibit Metabolic Specialization among Cosmopolitan and Endemic Populations.
SL Garcia, M Mehrshad, M Buck, JM Tsuji, JD Neufeld, KD McMahon, S Bertilsson, C Greening, S Peura
mSystems, 6 (3) 2379-5077 (2021)
Photosynthetic bacteria from the class Chlorobia (formerly phylum Chlorobi) sustain carbon fixation in anoxic water columns. They harvest light at extremely low intensities and use various inorganic electron donors to fix carbon dioxide into biomass. Until now, most information on the functional ecology and local adaptations of Chlorobia members came from isolates and merely 26 sequenced genomes that may not adequately represent natural populations. To address these limitations, we analyzed global metagenomes to profile planktonic Chlorobia cells from the oxyclines of 42 freshwater bodies, spanning subarctic to tropical regions and encompassing all four seasons. We assembled and compiled over 500 genomes, including metagenome-assembled genomes (MAGs), single-amplified genomes (SAGs), and reference genomes from cultures, clustering them into 71 metagenomic operational taxonomic units (mOTUs or "species"). Of the 71 mOTUs, 57 were classified within the genus Chlorobium, and these mOTUs represented up to ∼60% of the microbial communities in the sampled anoxic waters. Several Chlorobium-associated mOTUs were globally distributed, whereas others were endemic to individual lakes. Although most clades encoded the ability to oxidize hydrogen, many lacked genes for the oxidation of specific sulfur and iron substrates. Surprisingly, one globally distributed Scandinavian clade encoded the ability to oxidize hydrogen, sulfur, and iron, suggesting that metabolic versatility facilitated such widespread colonization. Overall, these findings provide new insight into the biogeography of the Chlorobia and the metabolic traits that facilitate niche specialization within lake ecosystems.IMPORTANCE The reconstruction of genomes from metagenomes has helped explore the ecology and evolution of environmental microbiota. We applied this approach to 274 metagenomes collected from diverse freshwater habitats that spanned oxic and anoxic zones, sampling seasons, and latitudes. We demonstrate widespread and abundant distributions of planktonic Chlorobia-associated bacteria in hypolimnetic waters of stratified freshwater ecosystems and show they vary in their capacities to use different electron donors. Having photoautotrophic potential, these Chlorobia members could serve as carbon sources that support metalimnetic and hypolimnetic food webs.
Antimicrobial peptide and sequence variation along a latitudinal gradient in two anurans.
M Cortázar-Chinarro, Y Meyer-Lucht, T Van der Valk, A Richter-Boix, A Laurila, J Höglund
BMC Genet., 21 (1) 1471-2156 (2020)
While there is evidence of both purifying and balancing selection in immune defense genes, large-scale genetic diversity in antimicrobial peptides (AMPs), an important part of the innate immune system released from dermal glands in the skin, has remained uninvestigated. Here we describe genetic diversity at three AMP loci (Temporin, Brevinin and Palustrin) in two ranid frogs (Rana arvalis and R. temporaria) along a 2000 km latitudinal gradient. We amplified and sequenced part of the Acidic Propiece domain and the hypervariable Mature Peptide domain (~ 150-200 bp) in the three genes using Illumina Miseq and expected to find decreased AMP genetic variation towards the northern distribution limit of the species similarly to studies on MHC genetic patterns.
We found multiple loci for each AMP and relatively high gene diversity, but no clear pattern of geographic genetic structure along the latitudinal gradient. We found evidence of trans-specific polymorphism in the two species, indicating a common evolutionary origin of the alleles. Temporin and Brevinin did not form monophyletic clades suggesting that they belong to the same gene family. By implementing codon evolution models we found evidence of strong positive selection acting on the Mature Peptide. We also found evidence of diversifying selection as indicated by divergent allele frequencies among populations and high Theta k values.
Our results suggest that AMPs are an important source of adaptive diversity, minimizing the chance of microorganisms developing resistance to individual peptides.
Transcription profiling of peripheral B cells in antibody-positive primary Sjögren's syndrome reveals upregulated expression of CX3CR1 and a type I and type II interferon signature.
J Imgenberg-Kreuz, JK Sandling, A Björk, J Nordlund, M Kvarnström, ML Eloranta, L Rönnblom, M Wahren-Herlenius, AC Syvänen, G Nordmark
Scand. J. Immunol., 87 (5) 1365-3083 (2018)
B cells play a key role in the pathogenesis of primary Sjögren's syndrome (pSS). The aim of this study was to analyse the transcriptome of CD19+ B cells from patients with pSS and healthy controls to decipher the B cell-specific contribution to pSS. RNA from purified CD19+ B cells from 12 anti-SSA antibody-positive untreated female patients with pSS and 20 healthy blood donors was subjected to whole transcriptome sequencing. A false discovery rate corrected significance threshold of α < 0.05 was applied to define differential gene expression. As validation, gene expression in B cells from 17 patients with pSS and 16 healthy controls was analysed using a targeted gene panel. RNA-sequencing identified 4047 differentially expressed autosomal genes in pSS B cells. Upregulated expression of type I and type II interferon (IFN)-induced genes was observed, establishing an IFN signature in pSS B cells. Among the top upregulated and validated genes were CX3CR1, encoding the fractalkine receptor involved in regulation of B-cell malignancies, CCL5/RANTES and CCR1. Increased expression of several members of the TNF superfamily was also identified; TNFSF4/Ox40L, TNFSF10/TRAIL, TNFSF13B/BAFF, TNFRSF17/BCMA as well as S100A8 and -A9/calprotectin, TLR7, STAT1 and STAT2. Among genes with downregulated expression in pSS B cells were SOCS1 and SOCS3, CD70 and TNFAIP3/A20. We conclude that B cells from patients with anti-SSA antibody-positive pSS display immune activation with upregulated expression of chemokines, chemokine receptors and a prominent type I and type II IFN signature, while suppressors of cytokine signalling are downregulated. This adds insight into the autoimmune process and suggests potential targets for future functional studies.
In recent years, nucleotide sequencing has become increasingly instrumental in both research and clinical settings. This has led to an explosive growth in sequencing data produced worldwide. As the amount of data increases, so does the need for automated solutions for data processing and analysis. The concept of workflows has gained favour in the bioinformatics community, but there is little in the scientific literature describing end-to-end automation systems. Arteria is an automation system that aims at providing a solution to the data-related operational challenges that face sequencing core facilities.
Arteria is built on existing open source technologies, with a modular design allowing for a community-driven effort to create plug-and-play micro-services. In this article we describe the system, elaborate on the underlying conceptual framework, and present an example implementation. Arteria can be reduced to 3 conceptual levels: orchestration (using an event-based model of automation), process (the steps involved in processing sequencing data, modelled as workflows), and execution (using a series of RESTful micro-services). This creates a system that is both flexible and scalable. Arteria-based systems have been successfully deployed at 3 sequencing core facilities. The Arteria Project code, written largely in Python, is available as open source software, and more information can be found at https://arteria-project.github.io/ .
We describe the Arteria system and the underlying conceptual framework, demonstrating how this model can be used to automate data handling and analysis in the context of a sequencing core facility.
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