Publications 2010

The Genomic HyperBrowser: inferential genomics at the sequence level.

Sandve GK, Gundersen S, Rydbeck H, Glad IK, Holden L, Holden M, Liestøl K, Clancy T, Ferkingstad E, Johansen M, Nygaard V, Tøstesen E, Frigessi A, Hovig E.
Genome Biol. 2010 Dec 23;11(12):R121. [Epub ahead of print]

PMID: 21182759

Cooperative epigenetic modulation by cancer amplicon genes.

Rui L, Emre NC, Kruhlak MJ, Chung HJ, Steidl C, Slack G, Wright GW, Lenz G, Ngo VN, Shaffer AL, Xu W, Zhao H, Yang Y, Lamy L, Davis RE, Xiao W, Powell J, Maloney D, Thomas CJ, Möller P, Rosenwald A, Ott G, Muller-Hermelink HK, Savage K, Connors JM, Rimsza LM, Campo E, Jaffe ES, Delabie J, Smeland EB, Weisenburger DD, Chan WC, Gascoyne RD, Levens D, Staudt LM.
Cancer Cell. 2010 Dec 14;18(6):590-605.

PMID: 21156283

TGF-β-induced growth inhibition in B-cell lymphoma correlates with Smad1/5 signalling and constitutively active p38 MAPK.

Bakkebø M, Huse K, Hilden VI, Smeland EB, Oksvold MP.
BMC Immunol. 2010 Nov 23;11:57.

PMID: 21092277

Merging transcriptomics and metabolomics – advances in breast cancer profiling.

Borgan E, Sitter B, Lingjærde OC, Johnsen H, Lundgren S, Bathen TF, Sørlie T, Børresen-Dale AL, Gribbestad IS.
BMC Cancer. 2010 Nov 16;10:628.

PMID: 21080935

DNA sequence profiles of the colorectal cancer critical gene set KRAS-BRAF-PIK3CA-PTEN-TP53 related to age at disease onset.

Berg M, Danielsen SA, Ahlquist T, Merok MA, Ågesen TH, Vatn MH, Mala T, Sjo OH, Bakka A, Moberg I, Fetveit T, Mathisen Ø, Husby A, Sandvik O, Nesbakken A, Thiis-Evensen E, Lothe RA.
PLoS One. 2010 Nov 12;5(11):e13978.

PMID: 21103049

Molecularly Targeted Therapies for Colorectal Cancer: Strategies for Implementing Translational Research in Clinical Trials.

Zwierzina H, Bardelli A, Ciardiello F, Gariboldi M, Håkansson L, Lambrechts D, Lind GE, Loeffler-Ragg J, Schmoll H, Siena S, Tabernero J, Van Cutsem E.
Curr Opin Mol Ther. 2010 Dec;12(6):703-11.

PMID: 21154162

DNA ploidy heterogeneity in endometrial carcinoma: comparison between curettage and hysterectomy specimens.

Pradhan M, Abeler VM, Davidson B, Kildal W, Nybøen A, Tropé CG, Risberg B, Danielsen HE.
Int J Gynecol Pathol. 2010 Nov;29(6):572-8.

PMID: 20881853

Colorectal carcinomas with microsatellite instability display a different pattern of target gene mutations according to large bowel site of origin.

Pinheiro M, Ahlquist T, Danielsen SA, Lind GE, Veiga I, Pinto C, Costa VL, Afonso L, Sousa O, Fragoso M, Santos L, Henrique R, Lopes P, Lopes C, Lothe RA, Teixeira MR.
BMC Cancer. 2010 Oct 27;10(1):587.

PMID: 20979647

Three epigenetic biomarkers, GDF15, TMEFF2 and VIM, accurately predict bladder cancer from DNA-based analyses of urine samples.

Costa VL, Henrique R, Danielsen SA, Duarte-Pereira S, Eknaes M, Skotheim RI, Rodrigues A, Magalhães JS, Oliveira J, Lothe RA, Teixeira MR, Jeronimo C, Lind GE.
Clin Cancer Res. 2010 Dec 1;16(23):5842-51. Epub 2010 Oct 25.

PMID: 20975101

Divide and ProsPer: The emerging role of PtdIns3P in cytokinesis.

Nezis IP, Sagona AP, Schink KO, Stenmark H.
Trends Cell Biol. 2010 Nov;20(11):642-9. Epub 2010 Sep 27.

PMID: 20880709

Autophagy as a trigger for cell death: Autophagic degradation of inhibitor of apoptosis dBruce controls DNA fragmentation during late oogenesis in Drosophila.

Nezis IP, Shravage BV, Sagona AP, Johansen T, Baehrecke EH, Stenmark H.
Autophagy. 2010 Nov 16;6(8):1214-5. Epub 2010 Nov 16.

PMID: 20935512

Roles of fibroblast growth factor receptors in carcinogenesis.

Haugsten EM, Wiedlocha A, Olsnes S, Wesche J.
Mol Cancer Res. 2010 Nov;8(11):1439-52.

PMID: 21047773

Endocytosis and retrograde transport of Shiga toxin.

Sandvig K, Bergan J, Dyve AB, Skotland T, Torgersen ML.
Toxicon. 2010 Dec 15;56(7):1181-5. Epub 2009 Nov 29.

PMID: 19951719

Allele-specific copy number analysis of tumors.

Van Loo P, Nordgard SH, Lingjærde OC, Russnes HG, Rye IH, Sun W, Weigman VJ, Marynen P, Zetterberg A, Naume B, Perou CM, Børresen-Dale AL, Kristensen VN.
Proc Natl Acad Sci U S A. 2010 Sep 28;107(39):16910-5.

PMID: 20837533

Impact of DNA physical properties on local sequence bias of human mutation.

Nakken S, Rødland EA, Hovig E.
Hum Mutat. 2010 Dec;31(12):1316-25.

PMID: 20886615

Functional characterization of the protein C A267T mutation: evidence for impaired secretion due to defective intracellular transport.

Tjeldhorn L, Iversen N, Sandvig K, Bergan J, Sandset PM, Skretting G.
BMC Cell Biol. 2010 Sep 6;11(1):67. [Epub ahead of print]

PMID: 20815936

Anti-CD47 antibody synergizes with rituximab to promote phagocytosis and eradicate non-Hodgkin lymphoma.

Chao MP, Alizadeh AA, Tang C, Myklebust JH, Varghese B, Gill S, Jan M, Cha AC, Chan CK, Tan BT, Park CY, Zhao F, Kohrt HE, Malumbres R, Briones J, Gascoyne RD, Lossos IS, Levy R, Weissman IL, Majeti R.
Cell. 2010 Sep 3;142(5):699-713.

PMID: 20813259

Clostridium botulinum C2 toxin is internalized by clathrin- and Rho-dependent mechanisms.

Pust S, Barth H, Sandvig K.
Cell Microbiol. 2010 Dec;12(12):1809-20.

PMID: 20690924

Shiga toxin increases formation of clathrin-coated pits through Syk kinase.

Utskarpen A, Massol R, van Deurs B, Lauvrak SU, Kirchhausen T, Sandvig K.
PLoS One. 2010 Jul 27;5(7):e10944.

PMID: 20668539

Array-CGH analysis of microdissected chromosome 19 markers in ovarian carcinoma identifies candidate target genes.

Micci F, Skotheim RI, Haugom L, Weimer J, Eibak AM, Abeler VM, Trope CG, Arnold N, Lothe RA, Heim S.
Genes Chromosomes Cancer. 2010 Nov;49(11):1046-53.

PMID: 20725991

UVRAG mutations associated with microsatellite unstable colon cancer do not affect autophagy.

Knævelsrud H, Ahlquist T, Merok MA, Nesbakken A, Stenmark H, Lothe RA, Simonsen A.
Autophagy. 2010 Oct 1;6(7):863-70.

PMID: 20724836

Time-resolved Ultrastructural Detection of Phosphatidylinositol 3-phosphate.

Stuffers S, Malerød L, Schink KO, Corvera S, Stenmark H, Brech A.
J Histochem Cytochem. 2010 Nov;58(11):1025-32.

PMID: 20713985

Autophagic degradation of dBruce controls DNA fragmentation in nurse cells during late Drosophila melanogaster oogenesis.

Nezis IP, Shravage BV, Sagona AP, Lamark T, Bjørkøy G, Johansen T, Rusten TE, Brech A, Baehrecke EH, Stenmark H.
J Cell Biol. 2010 Aug 23;190(4):523-31.

PMID: 20713604

Ubiquitination of alpha 5 beta 1 integrin controls fibroblast migration through lysosomal degradation of fibronectin-integrin complexes.

Lobert VH, Brech A, Pedersen NM, Wesche J, Oppelt A, Malerød L, Stenmark H.
Dev Cell. 2010 Jul 20;19(1):148-59.

PMID: 20643357

A phosphatidylinositol 3-kinase class III sub-complex containing VPS15, VPS34, Beclin 1, UVRAG and BIF-1 regulates cytokinesis and degradative endocytic traffic.

Thoresen SB, Pedersen NM, Liestøl K, Stenmark H.
Exp Cell Res. 2010 Dec 10;316(20):3368-78. Epub 2010 Jul 17.

PMID: 20643123

Genotypic and phenotypic classification of cancer: How should the impact of the two diagnostic approaches best be balanced?

Brandal P, Teixeira MR, Heim S.
Genes Chromosomes Cancer. 2010 Sep;49(9):763-74.

PMID: 20607708

The importance of gene-centring microarray data.

Sørlie T, Borgan E, Myhre S, Vollan HK, Russnes H, Zhao X, Nilsen G, Lingjaerde OC, Børresen-Dale AL, Rødland E.
Lancet Oncol. 2010 Aug;11(8):719-20; author reply 720-1.

PMID: 20688275

Expression levels of uridine 5′-diphospho-glucuronosyltransferase genes in breast tissue from healthy women are associated with mammographic density.

Haakensen VD, Biong M, Lingjærde OC, Holmen MM, Frantzen JO, Chen Y, Navjord D, Romundstad L, Lüders T, Bukholm IK, Solvang HK, Kristensen VN, Ursin G, Børresen-Dale AL, Helland A.
Breast Cancer Res. 2010;12(4):R65. Epub 2010 Aug 27.

PMID: 20799965

Molecular Mechanisms of Ubiquitin-Dependent Membrane Traffic.

Hurley JH, Stenmark H.
Annu Rev Biophys. 2010 Jul 21. [Epub ahead of print]

PMID: 21332354

STAMP1 Is Both a Proliferative and an Antiapoptotic Factor in Prostate Cancer.

Wang L, Jin Y, Arnoldussen YJ, Jonson I, Qu S, Mælandsmo GM, Kristian A, Risberg B, Wæhre H, Danielsen HE, Saatcioglu F.
Cancer Res. 2010 Jul 15;70(14):5818-28.

PMID: 20587517

Genomic alterations reveal potential for higher grade transformation in follicular lymphoma and confirm parallel evolution of tumor cell clones.

Eide MB, Liestol K, Lingjaerde OC, Hystad ME, Kresse SH, Meza-Zepeda L, Myklebost O, Trøen G, Aamot HV, Holte H, Smeland EB, Delabie J.
Blood. 2010 Sep 2;116(9):1489-97.

PMID: 20505157

Inhibition of Connexin43 gap junction channels by the endocrine disruptor ioxynil.

Leithe E, Kjenseth A, Bruun J, Sirnes S, Rivedal E.
Toxicol Appl Pharmacol. 2010 Aug 15;247(1):10-7.

PMID: 20510257

CIN85 regulates dopamine receptor endocytosis and governs behaviour in mice.

Shimokawa N, Haglund K, Hölter SM, Grabbe C, Kirkin V, Koibuchi N, Schultz C, Rozman J, Hoeller D, Qiu CH, Londoño MB, Ikezawa J, Jedlicka P, Stein B, Schwarzacher SW, Wolfer DP, Ehrhardt N, Heuchel R, Nezis I, Brech A, Schmidt MH, Fuchs H, Gailus-Durner V, Klingenspor M, Bogler O, Wurst W, Deller T, de Angelis MH, Dikic I.
EMBO J. 2010 Jul 21;29(14):2421-32.

PMID: 20551902

New metal-based nanoparticles for intravenous use: requirements for clinical success with focus on medical imaging.

Skotland T, Iversen TG, Sandvig K.
Nanomedicine. 2010 Dec;6(6):730-7. Epub 2010 May 26.

PMID: 20570639

Genomic architecture characterizes tumor progression paths and fate in breast cancer patients.

Russnes HG, Vollan HK, Lingjaerde OC, Krasnitz A, Lundin P, Naume B, Sørlie T, Borgen E, Rye IH, Langerød A, Chin SF, Teschendorff AE, Stephens PJ, Månér S, Schlichting E, Baumbusch LO, Kåresen R, Stratton MP, Wigler M, Caldas C, Zetterberg A, Hicks J, Børresen-Dale AL.
Sci Transl Med. 2010 Jun 30;2(38):38ra47.

PMID: 20592421

B-cell signaling networks reveal a negative prognostic human lymphoma cell subset that emerges during tumor progression.

Irish JM, Myklebust JH, Alizadeh AA, Houot R, Sharman JP, Czerwinski DK, Nolan GP, Levy R.
Proc Natl Acad Sci U S A. 2010 Jul 20;107(29):12747-54. Epub 2010 Jun 11.

PMID: 20543139

Protein secretion: unconventional exit by exophagy.

Abrahamsen H, Stenmark H.
Curr Biol. 2010 May 11;20(9):R415-8.

PMID: 20462486

Distinct high resolution genome profiles of early onset and late onset colorectal cancer integrated with gene expression data identify candidate susceptibility loci.

Berg M, Agesen TH, Thiis-Evensen E, Infac IS, Merok MA, Teixeira MR, Vatn MH, Nesbakken A, Skotheim RI, Lothe RA.
Mol Cancer. 2010 May 6;9(1):100.

PMID: 20459617

Expression pattern of the septin gene family in acute myeloid leukemias with and without MLL-SEPT fusion genes.

Santos J, Cerveira N, Bizarro S, Ribeiro FR, Correia C, Torres L, Lisboa S, Vieira J, Mariz JM, Norton L, Snijder S, Mellink CH, Buijs A, Shih LY, Strehl S, Micci F, Heim S, Teixeira MR.
Leuk Res. 2010 May;34(5):615-21.

PMID: 19748670

Cytokinesis and cancer.

Sagona AP, Stenmark H.
FEBS Lett. 2010 Jun 18;584(12):2652-61.

PMID: 20371245

Cindr interacts with anillin to control cytokinesis in Drosophila melanogaster.

Haglund K, Nezis IP, Lemus D, Grabbe C, Wesche J, Liestøl K, Dikic I, Palmer R, Stenmark H.
Curr Biol. 2010 May 25;20(10):944-50. Epub 2010 May 6.

PMID: 20451383

The selective macroautophagic degradation of aggregated proteins requires the PI3P-binding protein Alfy.

Filimonenko M, Isakson P, Finley KD, Anderson M, Jeong H, Melia TJ, Bartlett BJ, Myers KM, Birkeland HC, Lamark T, Krainc D, Brech A, Stenmark H, Simonsen A, Yamamoto A.
Mol Cell. 2010 Apr 23;38(2):265-79.

PMID: 20417604

PtdIns(3)P controls cytokinesis through KIF13A-mediated recruitment of FYVE-CENT to the midbody.

Sagona AP, Nezis IP, Pedersen NM, Liestøl K, Poulton J, Rusten TE, Skotheim RI, Raiborg C, Stenmark H.
Nat Cell Biol. 2010 Apr;12(4):362-71. Epub 2010 Mar 7.

PMID: 20208530

p62/SQSTM1 and ALFY interact to facilitate the formation of p62 bodies/ALIS and their degradation by autophagy.

Clausen TH, Lamark T, Isakson P, Finley K, Larsen KB, Brech A, Øvervatn A, Stenmark H, Bjørkøy G, Simonsen A, Johansen T.
Autophagy. 2010 Apr;6(3):330-44. Epub 2010 Apr 11.

PMID: 20168092

Protein toxins from plants and bacteria: Probes for intracellular transport and tools in medicine.

Sandvig K, Torgersen ML, Engedal N, Skotland T, Iversen TG.
FEBS Lett. 2010 Jun 18;584(12):2626-34.

PMID: 20385131

Glycan gene expression signatures in normal and malignant breast tissue; possible role in diagnosis and progression.

Potapenko IO, Haakensen VD, Lüders T, Helland A, Bukholm I, Sørlie T, Kristensen VN, Lingjaerde OC, Børresen-Dale AL.
Mol Oncol. 2010 Apr;4(2):98-118.

PMID: 20060370

p62, an autophagy hero or culprit?

Rusten TE, Stenmark H.
Nat Cell Biol. 2010 Mar;12(3):207-9.

PMID: 20190829

Genomic changes in chromosomes 10, 16, and X in malignant peripheral nerve sheath tumors identify a high-risk patient group.

Brekke HR, Ribeiro FR, Kolberg M, Agesen TH, Lind GE, Eknaes M, Hall KS, Bjerkehagen B, van den Berg E, Teixeira MR, Mandahl N, Smeland S, Mertens F, Skotheim RI, Lothe RA.
J Clin Oncol. 2010 Mar 20;28(9):1573-82. Epub 2010 Feb 16.

PMID: 20159821

Gap junction intercellular communication and benzene toxicity.

Rivedal E, Witz G, Leithe E.
Chem Biol Interact. 2010 Mar 19;184(1-2):229-32. Epub 2009 Nov 22.

PMID: 19932693

Unstable DNA repair genes shaped by their own sequence modifying phenotypes.

Falster DS, Nakken S, Bergem-Ohr M, Rødland EA, Breivik J.
J Mol Evol. 2010 Mar;70(3):266-74.

PMID: 20213140

ESCRT & Co.

Roxrud I, Stenmark H, Malerød L.
Biol Cell. 2010 Mar 12;102(5):293-318.

PMID: 20222872

The intracellular journey of Shiga toxins.

Torgersen ML, Engedal N, Bergan J, Sandvig K.
Open Toxinology Journal, 3, 3-12

Spindle proteins are differentially expressed in the various histological subtypes of testicular germ cell tumors.

Burum-Auensen E, Skotheim RI, Schjølberg AR, Røislien J, Lothe RA, Clausen OP.
J Carcinog. 2010 Mar 4;9:1.

PMID: 20411023

Regulation of gap junction intercellular communication by the ubiquitin system.

Kjenseth A, Fykerud T, Rivedal E, Leithe E.
Cell Signal. 2010 Sep;22(9):1267-73.

PMID: 20206687

Genomic aberrations in borderline ovarian tumors.

Micci F, Haugom L, Ahlquist T, Andersen HK, Abeler VM, Davidson B, Trope CG, Lothe RA, Heim S.
J Transl Med. 2010 Feb 26;8:21.

PMID: 20184781

CD81 protein is expressed at high levels in normal germinal center B cells and in subtypes of human lymphomas.

Luo RF, Zhao S, Tibshirani R, Myklebust JH, Sanyal M, Fernandez R, Gratzinger D, Marinelli RJ, Lu ZS, Wong A, Levy R, Levy S, Natkunam Y.
Hum Pathol. 2010 Feb;41(2):271-80. Epub 2009 Dec 8.

PMID: 20004001

Sialic acid-binding dwarf elder four-chain lectin displays nucleic acid N-glycosidase activity.

Iglesias R, Citores L, Ferreras JM, Pérez Y, Jiménez P, Gayoso MJ, Olsnes S, Tamburino R, Di Maro A, Parente A, Girbés T.
Biochimie. 2010 Jan;92(1):71-80. Epub 2009 Sep 30.

PMID: 19799962

Ultrastructural characterization of giant endosomes induced by GTPase-deficient Rab5.

Wegner CS, Malerød L, Pedersen NM, Progida C, Bakke O, Stenmark H, Brech A.
Histochem Cell Biol. 2010 Jan;133(1):41-55. Epub 2009 Oct 15.

PMID: 19830447

An inhibitory role of the G-protein regulator AGS3 in mTOR-dependent macroautophagy.

Groves B, Abrahamsen H, Clingan H, Frantz M, Mavor L, Bailey J, Ma D.
PLoS One. 2010 Jan 26;5(1):e8877.

PMID: 20126274

FYCO1 is a Rab7 effector that binds to LC3 and PI3P to mediate microtubule plus end-directed vesicle transport.

Pankiv S, Alemu EA, Brech A, Bruun JA, Lamark T, Overvatn A, Bjørkøy G, Johansen T.
J Cell Biol. 2010 Jan 25;188(2):253-69.

PMID: 20100911

Endocytosis and intracellular trafficking of quantum dot-ligand bioconjugates.

Iversen TG, Frerker N, Sandvig K
In Organelle-Specific Pharmaceutical Nanotechnology (Weissig V, D’Souza GG. eds., ISBN 978-0-470-63165-2)), pp. 55-72, Wiley & Sons, New Jersey, USA, October 2010.

The B[a]P-increased intercellular communication via translocation of connexin-43 into gap junctions reduces apoptosis.

Tekpli X, Rivedal E, Gorria M, Landvik NE, Rissel M, Dimanche-Boitrel MT, Baffet G, Holme JA, Lagadic-Gossmann D.
Toxicol Appl Pharmacol. 2010 Jan 15;242(2):231-40. Epub 2009 Oct 27.

PMID: 19874837

Interplay between toxic transport and flotillin localization.

Pust S, Dyve AB, Torgersen ML, van Deurs B, Sandvig K.
PLoS One. 2010 Jan 22;5(1):e8844.

PMID: 20107503

Chronic active B-cell-receptor signalling in diffuse large B-cell lymphoma.

Davis RE, Ngo VN, Lenz G, Tolar P, Young RM, Romesser PB, Kohlhammer H, Lamy L, Zhao H, Yang Y, Xu W, Shaffer AL, Wright G, Xiao W, Powell J, Jiang JK, Thomas CJ, Rosenwald A, Ott G, Muller-Hermelink HK, Gascoyne RD, Connors JM, Johnson NA, Rimsza LM, Campo E, Jaffe ES, Wilson WH, Delabie J, Smeland EB, Fisher RI, Braziel RM, Tubbs RR, Cook JR, Weisenburger DD, Chan WC, Pierce SK, Staudt LM.
Nature. 2010 Jan 7;463(7277):88-92.

PMID: 20054396

Tumor spreading to the contralateral ovary in bilateral ovarian carcinoma is a late event in clonal evolution.

Micci F, Haugom L, Ahlquist T, Abeler VM, Trope CG, Lothe RA, Heim S.
J Oncol. 2010;2010:646340. Epub 2009 Sep 15.

PMID: 19759843