Saturday, 29 September 2012

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Saturday, 2012 September 29
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.


PubMed Results
Items 1 - 3 of 3

1. Nature. 2012 Aug 23;488(7412):495-8. doi: 10.1038/nature11324.

Contrasting patterns of early twenty-first-century glacier mass change in the Himalayas.

Kääb A, Berthier E, Nuth C, Gardelle J, Arnaud Y .

Source

Department of Geosciences, University of Oslo, PO Box 1047, Blindern, 0316 Oslo, Norway. kaeaeb@geo.uio.no

Comment in

Abstract

Glaciers are among the best indicators of terrestrial climate variability, contribute importantly to water resources in many mountainous regions and are a major contributor to global sea level rise. In the Hindu Kush-Karakoram-Himalaya region (HKKH), a paucity of appropriate glacier data has prevented a comprehensive assessment of current regional mass balance. There is, however, indirect evidence of a complex pattern of glacial responses in reaction to heterogeneous climate change signals. Here we use satellite laser altimetry and a global elevation model to show widespread glacier wastage in the eastern, central and south-western parts of the HKKH during 2003-08. Maximal regional thinning rates were 0.66 ± 0.09 metres per year in the Jammu-Kashmir region. Conversely, in the Karakoram, glaciers thinned only slightly by a few centimetres per year. Contrary to expectations, regionally averaged thinning rates under debris-mantled ice were similar to those of clean ice despite insulation by debris covers. The 2003-08 specific mass balance for our entire HKKH study region was -0.21 ± 0.05 m yr(-1) water equivalent, significantly less negative than the estimated global average for glaciers and ice caps. This difference is mainly an effect of the balanced glacier mass budget in the Karakoram. The HKKH sea level contribution amounts to one per cent of the present-day sea level rise. Our 2003-08 mass budget of -12.8 ± 3.5 gigatonnes (Gt) per year is more negative than recent satellite-gravimetry-based estimates of -5 ± 3 Gt yr(-1) over 2003-10 (ref. 12). For the mountain catchments of the Indus and Ganges basins, the glacier imbalance contributed about 3.5% and about 2.0%, respectively, to the annual average river discharge, and up to 10% for the Upper Indus basin.

PMID: 22914167 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


2. Nature. 2012 Aug 23;488(7412):468-9. doi: 10.1038/488468a.

Climate science: Himalayan glaciers in the balance.

Cogley JG.

Comment on

PMID: 22914162 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


3. Nature. 2012 Aug 23;488(7412):508-11.

TNF receptor 1 genetic risk mirrors outcome of anti-TNF therapy in multiple sclerosis.

Gregory AP, Dendrou CA, Attfield KE, Haghikia A, Xifara DK, Butter F, Poschmann G, Kaur G, Lambert L, Leach OA, Prömel S, Punwani D, Felce JH, Davis SJ, Gold R, Nielsen FC, Siegel RM, Mann M, Bell JI, McVean G, Fugger L.

Source

MRC Human Immunology Unit, Weatherall Institute of Molecular Medicine, John Radcliffe Hospital, University of Oxford, Oxford OX3 9DS, UK.

Abstract

Although there has been much success in identifying genetic variants associated with common diseases using genome-wide association studies (GWAS), it has been difficult to demonstrate which variants are causal and what role they have in disease. Moreover, the modest contribution that these variants make to disease risk has raised questions regarding their medical relevance. Here we have investigated a single nucleotide polymorphism (SNP) in the TNFRSF1A gene, that encodes tumour necrosis factor receptor 1 (TNFR1), which was discovered through GWAS to be associated with multiple sclerosis (MS), but not with other autoimmune conditions such as rheumatoid arthritis, psoriasis and Crohn's disease. By analysing MS GWAS data in conjunction with the 1000 Genomes Project data we provide genetic evidence that strongly implicates this SNP, rs1800693, as the causal variant in the TNFRSF1A region. We further substantiate this through functional studies showing that the MS risk allele directs expression of a novel, soluble form of TNFR1 that can block TNF. Importantly, TNF-blocking drugs can promote onset or exacerbation of MS, but they have proven highly efficacious in the treatment of autoimmune diseases for which there is no association with rs1800693. This indicates that the clinical experience with these drugs parallels the disease association of rs1800693, and that the MS-associated TNFR1 variant mimics the effect of TNF-blocking drugs. Hence, our study demonstrates that clinical practice can be informed by comparing GWAS across common autoimmune diseases and by investigating the functional consequences of the disease-associated genetic variation.

PMID: 22801493 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


Tuesday, 25 September 2012

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Tuesday, 2012 September 25
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.


PubMed Results
Items 1 - 3 of 3

1. Nature. 2012 Aug 16;488(7411):269-71. doi: 10.1038/488269a.

Science on the Silk Road: Taste for adventure.

Abbott A.
PMID: 22895316 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


2. Nature. 2012 Aug 16;488(7411):404-8.

A selective jumonji H3K27 demethylase inhibitor modulates the proinflammatory macrophage response.

Kruidenier L, Chung CW, Cheng Z, Liddle J, Che K, Joberty G, Bantscheff M, Bountra C, Bridges A, Diallo H, Eberhard D, Hutchinson S, Jones E, Katso R, Leveridge M, Mander PK, Mosley J, Ramirez-Molina C, Rowland P, Schofield CJ, Sheppard RJ, Smith JE, Swales C, Tanner R, Thomas P, Tumber A, Drewes G, Oppermann U, Patel DJ, Lee K , Wilson DM.

Source

Epinova DPU, Immuno-Inflammation Therapy Area, GlaxoSmithKline R&D, Medicines Research Centre, Stevenage SG1 2NY, UK.

Abstract

The jumonji (JMJ) family of histone demethylases are Fe2+- and α-ketoglutarate-dependent oxygenases that are essential components of regulatory transcriptional chromatin complexes. These enzymes demethylate lysine residues in histones in a methylation-state and sequence-specific context. Considerable effort has been devoted to gaining a mechanistic understanding of the roles of histone lysine demethylases in eukaryotic transcription, genome integrity and epigenetic inheritance, as well as in development, physiology and disease. However, because of the absence of any selective inhibitors, the relevance of the demethylase activity of JMJ enzymes in regulating cellular responses remains poorly understood. Here we present a structure-guided small-molecule and chemoproteomics approach to elucidating the functional role of the H3K27me3-specific demethylase subfamily (KDM6 subfamily members JMJD3 and UTX). The liganded structures of human and mouse JMJD3 provide novel insight into the specificity determinants for cofactor, substrate and inhibitor recognition by the KDM6 subfamily of demethylases. We exploited these structural features to generate the first small-molecule catalytic site inhibitor that is selective for the H3K27me3-specific JMJ subfamily. We demonstrate that this inhibitor binds in a novel manner and reduces lipopolysaccharide-induced proinflammatory cytokine production by human primary macrophages, a process that depends on both JMJD3 and UTX. Our results resolve the ambiguity associated with the catalytic function of H3K27-specific JMJs in regulating disease-relevant inflammatory responses and provide encouragement for designing small-molecule inhibitors to allow selective pharmacological intervention across the JMJ family.

PMID: 22842901 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


3. Nature. 2012 Aug 16;488(7411):370-4.

Reconstructing Native American population history.

Reich D, Patterson N, Campbell D, Tandon A, Mazieres S, Ray N, Parra MV, Rojas W, Duque C, Mesa N, García LF, Triana O, Blair S, Maestre A, Dib JC, Bravi CM, Bailliet G, Corach D, Hünemeier T, Bortolini MC, Salzano FM, Petzl-Erler ML, Acuña-Alonzo V, Aguilar-Salinas C, Canizales-Quinteros S, Tusié-Luna T, Riba L, Rodríguez-Cruz M, Lopez-Alarcón M, Coral-Vazquez R, Canto-Cetina T, Silva-Zolezzi I, Fernandez-Lopez JC, Contreras AV, Jimenez-Sanchez G, Gómez-Vázquez MJ, Molina J, Carracedo A, Salas A, Gallo C, Poletti G, Witonsky DB, Alkorta-Aranburu G, Sukernik RI, Osipova L, Fedorova SA, Vasquez R, Villena M, Moreau C, Barrantes R, Pauls D, Excoffier L, Bedoya G, Rothhammer F, Dugoujon JM, Larrouy G, Klitz W, Labuda D, Kidd J, Kidd K, Di Rienzo A, Freimer NB, Price AL, Ruiz-Linares A.

Source

Department of Genetics, Harvard Medical School, Boston, Massachusetts 02115, USA. reich@genetics.med.harvard.edu

Abstract

The peopling of the Americas has been the subject of extensive genetic, archaeological and linguistic research; however, central questions remain unresolved. One contentious issue is whether the settlement occurred by means of a single migration or multiple streams of migration from Siberia. The pattern of dispersals within the Americas is also poorly understood. To address these questions at a higher resolution than was previously possible, we assembled data from 52 Native American and 17 Siberian groups genotyped at 364,470 single nucleotide polymorphisms. Here we show that Native Americans descend from at least three streams of Asian gene flow. Most descend entirely from a single ancestral population that we call 'First American'. However, speakers of Eskimo-Aleut languages from the Arctic inherit almost half their ancestry from a second stream of Asian gene flow, and the Na-Dene-speaking Chipewyan from Canada inherit roughly one-tenth of their ancestry from a third stream. We show that the initial peopling followed a southward expansion facilitated by the coast, with sequential population splits and little gene flow after divergence, especially in South America. A major exception is in Chibchan speakers on both sides of the Panama isthmus, who have ancestry from both North and South America.

PMID: 22801491 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


Thursday, 20 September 2012

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Thursday, 2012 September 20
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.


PubMed Results
Items 1 - 8 of 8

1. Nat Med. 2012 Jul 6;18(7):1041-51. doi: 10.1038/nm.2829.

From prenatal genomic diagnosis to fetal personalized medicine: progress and challenges.

Bianchi DW.

Source

The Mother Infant Research Institute at Tufts Medical Center and the Division of Genetics, Department of Pediatrics, Floating Hospital for Children, Boston, Massachusetts, USA. dbianchi@tuftsmedicalcenter.org

Abstract

Thus far, the focus of personalized medicine has been the prevention and treatment of conditions that affect adults. Although advances in genetic technology have been applied more frequently to prenatal diagnosis than to fetal treatment, genetic and genomic information is beginning to influence pregnancy management. Recent developments in sequencing the fetal genome combined with progress in understanding fetal physiology using gene expression arrays indicate that we could have the technical capabilities to apply an individualized medicine approach to the fetus. Here I review recent advances in prenatal genetic diagnostics, the challenges associated with these new technologies and how the information derived from them can be used to advance fetal care. Historically, the goal of prenatal diagnosis has been to provide an informed choice to prospective parents. We are now at a point where that goal can and should be expanded to incorporate genetic, genomic and transcriptomic data to develop new approaches to fetal treatment.

PMID: 22772565 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


2. Nat Med. 2012 Jul 6;18(7):1002. doi: 10.1038/nm0712-1002.

Straight talk with...Phillip Dellinger. Interviewed by Roxanne Khamsi.

Dellinger P.
PMID: 22772544 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


3. Nat Med. 2012 Jul 6;18(7):1001. doi: 10.1038/nm0712-1001.

After Xigris, researchers look to new targets to combat sepsis.

Williams SC.
PMID: 22772543 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


4. Nat Med. 2012 Jul 6;18(7):1000. doi: 10.1038/nm0712-1000.

Trial failure prompts soul-searching for critical-care specialists.

Dolgin E.
PMID: 22772542 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


5. Nat Med. 2012 Jul 6;18(7):999. doi: 10.1038/nm0712-999.

New biomarkers sought for improving sepsis management and care.

Moyer MW.
PMID: 22772541 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


6. Nat Med. 2012 Jul 6;18(7):998-9. doi: 10.1038/nm0712-998b.

Execution of sepsis trials needs an overhaul, experts say.

Khamsi R.
PMID: 22772540 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


7. Nat Med. 2012 Jul 6;18(7):998. doi: 10.1038/nm0712-998a.

Rodent models of sepsis found shockingly lacking.

Raven K.
PMID: 22772539 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


8. Nat Med. 2012 Jul 6;18(7):997. doi: 10.1038/nm0712-997.

Focus on sepsis.

[No authors listed]
PMID: 22772538 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


Tuesday, 18 September 2012

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Tuesday, 2012 September 18
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.


PubMed Results
Items 1 - 4 of 4

1. Science. 2012 Sep 7;337(6099):1167-9.

Profile: Ewan Birney. Genomics' big talker.

Pennisi E.
PMID: 22955814 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


2. Science. 2012 Sep 7;337(6099):1159, 1161.

Genomics. ENCODE project writes eulogy for junk DNA.

Pennisi E.
PMID: 22955811 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


3. Science. 2012 Aug 31;337(6098):1107-11.

The shared antibiotic resistome of soil bacteria and human pathogens.

Forsberg KJ, Reyes A, Wang B, Selleck EM, Sommer MO, Dantas G.

Source

Center for Genome Sciences and Systems Biology, Washington University School of Medicine, St. Louis, MO 63108, USA.

Abstract

Soil microbiota represent one of the ancient evolutionary origins of antibiotic resistance and have been proposed as a reservoir of resistance genes available for exchange with clinical pathogens. Using a high-throughput functional metagenomic approach in conjunction with a pipeline for the de novo assembly of short-read sequence data from functional selections (termed PARFuMS), we provide evidence for recent exchange of antibiotic resistance genes between environmental bacteria and clinical pathogens. We describe multidrug-resistant soil bacteria containing resistance cassettes against five classes of antibiotics (β-lactams, aminoglycosides, amphenicols, sulfonamides, and tetracyclines) that have perfect nucleotide identity to genes from diverse human pathogens. This identity encompasses noncoding regions as well as multiple mobilization sequences, offering not only evidence of lateral exchange but also a mechanism by which antibiotic resistance disseminates.

PMID: 22936781 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


4. Science. 2012 Aug 31;337(6098):1036.

Immunology. Stalling sepsis?

Leslie M.
PMID: 22936753 [PubMed - indexed for MEDLINE]
Related citations


Saturday, 15 September 2012

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Saturday, 2012 September 15
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.


PubMed Results
Items 1 - 4 of 4

1. N Engl J Med. 2012 Sep 6;367(10):968-9; author reply 969.

Drotrecogin alfa (activated) in septic shock.

Nayyar V, Solano T.

Comment on

  • Drotrecogin alfa (activated) in adults with septic shock. [N Engl J Med. 2012]
PMID: 22931268 [PubMed - indexed for MEDLINE]
Related citations
Icon for Atypon


2. N Engl J Med. 2012 Sep 6;367(10):968; author reply 969.

Drotrecogin alfa (activated) in septic shock.

Hollander JE.

Comment on

  • Drotrecogin alfa (activated) in adults with septic shock. [N Engl J Med. 2012]
PMID: 22931267 [PubMed - indexed for MEDLINE]
Related citations
Icon for Atypon


3. Science. 2012 Aug 3;337(6094):531-2.

Systems biology. Modular biological complexity.

Koch C.

Source

Allen Institute for Brain Science, Seattle, WA 98103, USA. christofk@alleninstitute.org

PMID: 22859475 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


4. Science. 2012 Jun 1;336(6085):1112-3.

Medicine. Whole-genome sequencing: the new standard of care?

Brunham LR, Hayden MR.

Source

Department of Medicine, University of British Columbia, Vancouver, British Columbia V5Z 4H4, Canada.

Comment in

PMID: 22654044 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


Friday, 14 September 2012

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Friday, 2012 September 14
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.


PubMed Results
Items 1 - 6 of 6

1. Science. 2012 Aug 24;337(6097):957-60.

Mapping the origins and expansion of the Indo-European language family.

Bouckaert R, Lemey P, Dunn M, Greenhill SJ, Alekseyenko AV, Drummond AJ, Gray RD, Suchard MA, Atkinson QD.

Source

Department of Computer Science, University of Auckland, Auckland 1142, New Zealand.

Comment in

Abstract

There are two competing hypotheses for the origin of the Indo-European language family. The conventional view places the homeland in the Pontic steppes about 6000 years ago. An alternative hypothesis claims that the languages spread from Anatolia with the expansion of farming 8000 to 9500 years ago. We used Bayesian phylogeographic approaches, together with basic vocabulary data from 103 ancient and contemporary Indo-European languages, to explicitly model the expansion of the family and test these hypotheses. We found decisive support for an Anatolian origin over a steppe origin. Both the inferred timing and root location of the Indo-European language trees fit with an agricultural expansion from Anatolia beginning 8000 to 9500 years ago. These results highlight the critical role that phylogeographic inference can play in resolving debates about human prehistory.

PMID: 22923579 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


2. Science. 2012 Aug 24;337(6097):967-71. Epub 2012 Jun 28.

Landscape of somatic retrotransposition in human cancers.

Lee E, Iskow R, Yang L, Gokcumen O, Haseley P, Luquette LJ 3rd, Lohr JG, Harris CC, Ding L, Wilson RK, Wheeler DA, Gibbs RA, Kucherlapati R, Lee C, Kharchenko PV, Park PJ; Cancer Genome Atlas Research Network.

Source

Center for Biomedical Informatics, Harvard Medical School, Boston, MA 02115, USA.

Abstract

Transposable elements (TEs) are abundant in the human genome, and some are capable of generating new insertions through RNA intermediates. In cancer, the disruption of cellular mechanisms that normally suppress TE activity may facilitate mutagenic retrotranspositions. We performed single-nucleotide resolution analysis of TE insertions in 43 high-coverage whole-genome sequencing data sets from five cancer types. We identified 194 high-confidence somatic TE insertions, as well as thousands of polymorphic TE insertions in matched normal genomes. Somatic insertions were present in epithelial tumors but not in blood or brain cancers. Somatic L1 insertions tend to occur in genes that are commonly mutated in cancer, disrupt the expression of the target genes, and are biased toward regions of cancer-specific DNA hypomethylation, highlighting their potential impact in tumorigenesis.

PMID: 22745252 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


3. Science. 2012 Apr 13;336(6078):179-82.

Integrating genomes.

Zerbino DR, Paten B, Haussler D.

Source

Center for Biomolecular Sciences and Engineering, University of California, Santa Cruz, CA 95064, USA.

Abstract

As genomic sequencing projects attempt ever more ambitious integration of genetic, molecular, and phenotypic information, a specialization of genomics has emerged, embodied in the subdiscipline of computational genomics. Models inherited from population genetics, phylogenetics, and human disease genetics merge with those from graph theory, statistics, signal processing, and computer science to provide a rich quantitative foundation for genomics that can only be realized with the aid of a computer. Unleashed on a rapidly increasing sample of the planet's 10(30) organisms, these analyses will have an impact on diverse fields of science while providing an extraordinary new window into the story of life.

PMID: 22499938 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


4. Science. 2012 Apr 13;336(6078):171.

Computational biology. Does it compute? Introduction.

Vinson V, Purnell BA, Zahn LM, Travis J.
PMID: 22499935 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


5. Science. 2012 Apr 13;336(6078):161-2.

Neuroscience. Revitalizing remyelination--the answer is circulating.

Redmond SA, Chan JR.

Source

Department of Neurology, University of California, San Francisco, CA 94158, USA.

PMID: 22499927 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


6. Science. 2012 Mar 9;335(6073):1183.

Retrospective. Roy J. Britten (1919-2012).

Davidson EH.

Source

California Institute of Technology, Pasadena, CA 91125, USA. davidson@caltech.edu

PMID: 22403381 [PubMed - indexed for MEDLINE]
Related citations
Icon for HighWire Press


Wednesday, 5 September 2012

What's new for 'JKB_daily1' in PubMed

This message contains My NCBI what's new results from the National Center for Biotechnology Information (NCBI) at the U.S. National Library of Medicine (NLM).
Do not reply directly to this message.

Sender's message: Sepsis or genomics or altitude: JKB_daily1

Sent on Wednesday, 2012 September 05
Search: (sepsis[MeSH Terms] OR septic shock[MeSH Terms] OR altitude[MeSH Terms] OR genomics[MeSH Terms] OR genetics[MeSH Terms] OR retrotransposons[MeSH Terms] OR macrophage[MeSH Terms]) AND ("2009/8/8"[Publication Date] : "3000"[Publication Date]) AND (("Science"[Journal] OR "Nature"[Journal] OR "The New England journal of medicine"[Journal] OR "Lancet"[Journal] OR "Nature genetics"[Journal] OR "Nature medicine"[Journal]) OR (Hume DA[Author] OR Baillie JK[Author] OR Faulkner, Geoffrey J[Author]))

Click here to view complete results in PubMed (Results may change over time.)
To unsubscribe from these e-mail updates click here.


PubMed Results
Items 1 - 4 of 4

1. Nature. 2012 Aug 2;488(7409):19. doi: 10.1038/488019a.

Geneticists eye the potential of arXiv.

Callaway E.
PMID: 22859182 [PubMed - indexed for MEDLINE]
Related citations


2. Nature. 2012 Aug 2;488(7409):100-5.

Dissecting the genomic complexity underlying medulloblastoma.

Jones DT, Jäger N, Kool M, Zichner T, Hutter B, Sultan M, Cho YJ, Pugh TJ, Hovestadt V, Stütz AM, Rausch T, Warnatz HJ, Ryzhova M, Bender S, Sturm D, Pleier S, Cin H, Pfaff E, Sieber L, Wittmann A, Remke M, Witt H, Hutter S, Tzaridis T, Weischenfeldt J, Raeder B, Avci M, Amstislavskiy V, Zapatka M, Weber UD, Wang Q, Lasitschka B, Bartholomae CC, Schmidt M, von Kalle C, Ast V, Lawerenz C, Eils J, Kabbe R, Benes V, van Sluis P, Koster J, Volckmann R, Shih D, Betts MJ, Russell RB, Coco S, Tonini GP, Schüller U, Hans V, Graf N, Kim YJ, Monoranu C, Roggendorf W, Unterberg A, Herold-Mende C, Milde T, Kulozik AE, von Deimling A, Witt O, Maass E, Rössler J, Ebinger M, Schuhmann MU, Frühwald MC, Hasselblatt M, Jabado N, Rutkowski S, von Bueren AO, Williamson D, Clifford SC, McCabe MG, Collins VP, Wolf S, Wiemann S, Lehrach H, Brors B, Scheurlen W, Felsberg J, Reifenberger G, Northcott PA, Taylor MD, Meyerson M, Pomeroy SL, Yaspo ML, Korbel JO, Korshunov A, Eils R, Pfister SM, Lichter P.

Source

Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), Im Neuenheimer Feld 280, Heidelberg 69120, Germany.

Abstract

Medulloblastoma is an aggressively growing tumour, arising in the cerebellum or medulla/brain stem. It is the most common malignant brain tumour in children, and shows tremendous biological and clinical heterogeneity. Despite recent treatment advances, approximately 40% of children experience tumour recurrence, and 30% will die from their disease. Those who survive often have a significantly reduced quality of life. Four tumour subgroups with distinct clinical, biological and genetic profiles are currently identified. WNT tumours, showing activated wingless pathway signalling, carry a favourable prognosis under current treatment regimens. SHH tumours show hedgehog pathway activation, and have an intermediate prognosis. Group 3 and 4 tumours are molecularly less well characterized, and also present the greatest clinical challenges. The full repertoire of genetic events driving this distinction, however, remains unclear. Here we describe an integrative deep-sequencing analysis of 125 tumour-normal pairs, conducted as part of the International Cancer Genome Consortium (ICGC) PedBrain Tumor Project. Tetraploidy was identified as a frequent early event in Group 3 and 4 tumours, and a positive correlation between patient age and mutation rate was observed. Several recurrent mutations were identified, both in known medulloblastoma-related genes (CTNNB1, PTCH1, MLL2, SMARCA4) and in genes not previously linked to this tumour (DDX3X, CTDNEP1, KDM6A, TBR1), often in subgroup-specific patterns. RNA sequencing confirmed these alterations, and revealed the expression of what are, to our knowledge, the first medulloblastoma fusion genes identified. Chromatin modifiers were frequently altered across all subgroups. These findings enhance our understanding of the genomic complexity and heterogeneity underlying medulloblastoma, and provide several potential targets for new therapeutics, especially for Group 3 and 4 patients.

PMID: 22832583 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


3. Nature. 2012 Aug 2;488(7409):49-56.

Subgroup-specific structural variation across 1,000 medulloblastoma genomes.

Northcott PA, Shih DJ, Peacock J, Garzia L, Morrissy AS, Zichner T, Stütz AM, Korshunov A, Reimand J, Schumacher SE, Beroukhim R, Ellison DW, Marshall CR, Lionel AC, Mack S, Dubuc A, Yao Y, Ramaswamy V, Luu B, Rolider A, Cavalli FM, Wang X, Remke M, Wu X, Chiu RY, Chu A, Chuah E, Corbett RD, Hoad GR, Jackman SD, Li Y, Lo A, Mungall KL, Nip KM, Qian JQ, Raymond AG, Thiessen NT, Varhol RJ, Birol I, Moore RA, Mungall AJ, Holt R, Kawauchi D, Roussel MF, Kool M, Jones DT, Witt H, Fernandez-L A, Kenney AM, Wechsler-Reya RJ, Dirks P, Aviv T, Grajkowska WA, Perek-Polnik M, Haberler CC, Delattre O, Reynaud SS, Doz FF, Pernet-Fattet SS, Cho BK, Kim SK, Wang KC, Scheurlen W, Eberhart CG, Fèvre-Montange M, Jouvet A, Pollack IF, Fan X, Muraszko KM, Gillespie GY, Di Rocco C, Massimi L, Michiels EM, Kloosterhof NK, French PJ, Kros JM, Olson JM, Ellenbogen RG, Zitterbart K, Kren L, Thompson RC, Cooper MK, Lach B, McLendon RE, Bigner DD, Fontebasso A, Albrecht S, Jabado N, Lindsey JC, Bailey S, Gupta N, Weiss WA, Bognár L, Klekner A, Van Meter TE, Kumabe T, Tominaga T, Elbabaa SK, Leonard JR, Rubin JB, Liau LM, Van Meir EG, Fouladi M, Nakamura H, Cinalli G, Garami M, Hauser P, Saad AG, Iolascon A, Jung S, Carlotti CG, Vibhakar R, Ra YS, Robinson S, Zollo M, Faria CC, Chan JA, Levy ML, Sorensen PH, Meyerson M, Pomeroy SL, Cho YJ, Bader GD, Tabori U, Hawkins CE, Bouffet E, Scherer SW, Rutka JT, Malkin D, Clifford SC, Jones SJ, Korbel JO, Pfister SM, Marra MA, Taylor MD.

Source

Developmental & Stem Cell Biology Program, The Hospital for Sick Children, Toronto, Ontario M5G 1L7, Canada.

Abstract

Medulloblastoma, the most common malignant paediatric brain tumour, is currently treated with nonspecific cytotoxic therapies including surgery, whole-brain radiation, and aggressive chemotherapy. As medulloblastoma exhibits marked intertumoural heterogeneity, with at least four distinct molecular variants, previous attempts to identify targets for therapy have been underpowered because of small samples sizes. Here we report somatic copy number aberrations (SCNAs) in 1,087 unique medulloblastomas. SCNAs are common in medulloblastoma, and are predominantly subgroup-enriched. The most common region of focal copy number gain is a tandem duplication of SNCAIP, a gene associated with Parkinson's disease, which is exquisitely restricted to Group 4α. Recurrent translocations of PVT1, including PVT1-MYC and PVT1-NDRG1, that arise through chromothripsis are restricted to Group 3. Numerous targetable SCNAs, including recurrent events targeting TGF-β signalling in Group 3, and NF-κB signalling in Group 4, suggest future avenues for rational, targeted therapy.

PMID: 22832581 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group


4. Nature. 2012 Aug 2;488(7409):43-8.

Novel mutations target distinct subgroups of medulloblastoma.

Robinson G, Parker M, Kranenburg TA, Lu C, Chen X, Ding L, Phoenix TN, Hedlund E, Wei L, Zhu X, Chalhoub N, Baker SJ, Huether R, Kriwacki R, Curley N, Thiruvenkatam R, Wang J, Wu G, Rusch M, Hong X, Becksfort J, Gupta P, Ma J, Easton J, Vadodaria B, Onar-Thomas A, Lin T, Li S, Pounds S, Paugh S, Zhao D, Kawauchi D, Roussel MF, Finkelstein D, Ellison DW, Lau CC, Bouffet E, Hassall T, Gururangan S, Cohn R, Fulton RS, Fulton LL, Dooling DJ, Ochoa K, Gajjar A, Mardis ER, Wilson RK, Downing JR, Zhang J, Gilbertson RJ.

Source

St Jude Children's Research Hospital, Washington University Pediatric Cancer Genome Project, Memphis, Tennessee 38105, USA.

Abstract

Medulloblastoma is a malignant childhood brain tumour comprising four discrete subgroups. Here, to identify mutations that drive medulloblastoma, we sequenced the entire genomes of 37 tumours and matched normal blood. One-hundred and thirty-six genes harbouring somatic mutations in this discovery set were sequenced in an additional 56 medulloblastomas. Recurrent mutations were detected in 41 genes not yet implicated in medulloblastoma; several target distinct components of the epigenetic machinery in different disease subgroups, such as regulators of H3K27 and H3K4 trimethylation in subgroups 3 and 4 (for example, KDM6A and ZMYM3), and CTNNB1-associated chromatin re-modellers in WNT-subgroup tumours (for example, SMARCA4 and CREBBP). Modelling of mutations in mouse lower rhombic lip progenitors that generate WNT-subgroup tumours identified genes that maintain this cell lineage (DDX3X), as well as mutated genes that initiate (CDH1) or cooperate (PIK3CA) in tumorigenesis. These data provide important new insights into the pathogenesis of medulloblastoma subgroups and highlight targets for therapeutic development.

PMCID: PMC3412905 [Available on 2013/2/2]
PMID: 22722829 [PubMed - indexed for MEDLINE]
Related citations
Icon for Nature Publishing Group