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university of tampere: faculty of medicine and life sciences: research: anne kallioniemi - cancer genomics:
Lääketieteen ja biotieteiden tiedekuntaUniversity of TampereLääketieteen ja biotieteiden tiedekunta
Anne Kallioniemi - Cancer Genomics

Previous publications

Kiiski JI, Fagerholm R, Tervasmäki A, Pelttari LM, Khan S, Jamshidi M, Mantere T, Pylkäs K, Bartek J, Bartkova J, Mannermaa A, Tengström M, Kosma VM, Winqvist R, Kallioniemi A, Aittomäki K, Blomqvist C, Nevanlinna H
FANCM c.5101C>T mutation associates with breast cancer survival and treatment outcome.
Int J Cancer ;139(12)2760-2770, 2016
PMID

Alarmo EL, Havunen R, Häyrynen S, Penkki S, Ketolainen J, Nykter M, Kallioniemi A
Bone morphogenetic protein 4 regulates microRNA expression in breast cancer cell lines in diverse fashion.
Genes Chromosomes Cancer ;55(3)227-36, 2016
PMID

Juuti-Uusitalo K, Nieminen M, Treumer F, Ampuja M, Kallioniemi A, Klettner A, Skottman H
Effects of Cytokine Activation and Oxidative Stress on the Function of the Human Embryonic Stem Cell-Derived Retinal Pigment Epithelial Cells.
Invest Ophthalmol Vis Sci 2015 ;56(11)6265-74
PMID

Kiiski JI, Pelttari LM, Khan S, Freysteinsdottir ES, Reynisdottir I, Hart SN, Shimelis H, Vilske S, Kallioniemi A, Schleutker J, Leminen A, Bützow R, Blomqvist C, Barkardottir RB, Couch FJ, Aittomäki K, Nevanlinna H
Exome sequencing identifies FANCM as a susceptibility gene for triple-negative breast cancer.
Proc Natl Acad Sci U S A 2014 ;111(42)15172-7
PMID

Antoniou AC, Casadei S, Heikkinen T, Barrowdale D, Pylkäs K, Roberts J, Lee A, Subramanian D, De Leeneer K, Fostira F, Tomiak E, Neuhausen SL, Teo ZL, Khan S, Aittomäki K, Moilanen JS, Turnbull C, Seal S, Mannermaa A, Kallioniemi A, Lindeman GJ, Buys SS, Andrulis IL, Radice P, Tondini C, Manoukian S, Toland AE, Miron P, Weitzel JN, Domchek SM, Poppe B, Claes KB, Yannoukakos D, Concannon P, Bernstein JL, James PA, Easton DF, Goldgar DE, Hopper JL, Rahman N, Peterlongo P, Nevanlinna H, King MC, Couch FJ, Southey MC, Winqvist R, Foulkes WD, Tischkowitz M
Breast-cancer risk in families with mutations in PALB2.
N Engl J Med 2014 ;371(6)497-506
PMID

Wikman H, Westphal L, Schmid F, Pollari S, Kropidlowski J, Sielaff-Frimpong B, Glatzel M, Matschke J, Westphal M, Iljin K, Huhtala H, Terracciano L, Kallioniemi A, Sauter G, Müller V, Witzel I, Lamszus K, Kemming D, Pantel K
Loss of CADM1 expression is associated with poor prognosis and brain metastasis in breast cancer patients.
Oncotarget 2014 ;5(10)3076-87
PMID

Heikkinen T, Khan S, Huovari E, Vilske S, Schleutker J, Kallioniemi A, Blomqvist C, Aittomäki K, Nevanlinna H
Evaluation of the RHINO gene for breast cancer predisposition in Finnish breast cancer families.
Breast Cancer Res Treat 2014 ;144(2)437-41
PMID

Laurila E, Vuorinen E, Savinainen K, Rauhala H, Kallioniemi A
KPNA7, a nuclear transport receptor, promotes malignant properties of pancreatic cancer cells in vitro.
Exp Cell Res 2014 ;322(1)159-67
PMID

Laurila E, Vuorinen E, Savinainen K, Rauhala H, Kallioniemi A
KPNA7, a nuclear transport receptor, promotes malignant properties of pancreatic cancer cells in vitro.
Exp Cell Res 2013 ;
PMID

Ampuja M, Jokimäki R, Juuti-Uusitalo K, Rodriguez-Martinez A, Alarmo EL, Kallioniemi A
BMP4 inhibits the proliferation of breast cancer cells and induces an MMP-dependent migratory phenotype in MDA-MB-231 cells in 3D environment.
BMC Cancer 2013 ;13429
PMID

Laurila EM, Kallioniemi A
The diverse role of miR-31 in regulating cancer associated phenotypes.
Genes Chromosomes Cancer 2013 ;
PMID

Laurila R, Parkkila S, Isola J, Kallioniemi A, Alarmo EL
The expression patterns of gremlin 1 and noggin in normal adult and tumor tissues.
Int J Clin Exp Pathol 2013 ;6(7)1400-8
PMID

Laitinen VH, Wahlfors T, Saaristo L, Rantapero T, Pelttari LM, Kilpivaara O, Laasanen SL, Kallioniemi A, Nevanlinna H, Aaltonen L, Vessella RL, Auvinen A, Visakorpi T, Tammela TL, Schleutker J
HOXB13 G84E mutation in Finland: population-based analysis of prostate, breast, and colorectal cancer risk.
Cancer Epidemiol Biomarkers Prev 2013 ;22(3)452-60
PMID

Rauhala HE, Teppo S, Niemelä S, Kallioniemi A
Silencing of the ARP2/3 complex disturbs pancreatic cancer cell migration.
Anticancer Res 2013 ;33(1)45-52
PMID

Alarmo EL, Huhtala H, Korhonen T, Pylkkänen L, Holli K, Kuukasjärvi T, Parkkila S, Kallioniemi A
Bone morphogenetic protein 4 expression in multiple normal and tumor tissues reveals its importance beyond development.
Mod Pathol 2013 ;26(1)10-21
PMID

Kallioniemi A
Bone morphogenetic protein 4-a fascinating regulator of cancer cell behavior.
Cancer Genet 2012 ;205(6)267-77
PMID

Pylkäs K, Vuorela M, Otsukka M, Kallioniemi A, Jukkola-Vuorinen A, Winqvist R
Rare copy number variants observed in hereditary breast cancer cases disrupt genes in estrogen signaling and TP53 tumor suppression network.
PLoS Genet 2012 ;8(6)e1002734
PMID

Pelttari LM, Kiiski J, Nurminen R, Kallioniemi A, Schleutker J, Gylfe A, Aaltonen LA, Leminen A, Heikkilä P, Blomqvist C, Bützow R, Aittomäki K, Nevanlinna H
A Finnish founder mutation in RAD51D: analysis in breast, ovarian, prostate, and colorectal cancer.
J Med Genet 2012 ;49(7)429-32
PMID

Solyom S, Aressy B, Pylkäs K, Patterson-Fortin J, Hartikainen JM, Kallioniemi A, Kauppila S, Nikkilä J, Kosma VM, Mannermaa A, Greenberg RA, Winqvist R
Breast cancer-associated Abraxas mutation disrupts nuclear localization and DNA damage response functions.
Sci Transl Med 2012 ;4(122)122ra23
PMID

Laurila EM, Sandström S, Rantanen LM, Autio R, Kallioniemi A
Both inhibition and enhanced expression of miR-31 lead to reduced migration and invasion of pancreatic cancer cells.
Genes Chromosomes Cancer 2012 ;51(6)557-68
PMID

Jin K, Kong X, Shah T, Penet MF, Wildes F, Sgroi DC, Ma XJ, Huang Y, Kallioniemi A, Landberg G, Bieche I, Wu X, Lobie PE, Davidson NE, Bhujwalla ZM, Zhu T, Sukumar S
The HOXB7 protein renders breast cancer cells resistant to tamoxifen through activation of the EGFR pathway.
Proc Natl Acad Sci U S A 2012 ;109(8)2736-41
PMID

Rodriguez-Martinez A, Alarmo EL, Saarinen L, Ketolainen J, Nousiainen K, Hautaniemi S, Kallioniemi A
Analysis of BMP4 and BMP7 signaling in breast cancer cells unveils time-dependent transcription patterns and highlights a common synexpression group of genes.
BMC Med Genomics 2011 ;480
PMID

Kallio H, Tolvanen M, Jänis J, Pan PW, Laurila E, Kallioniemi A, Kilpinen S, Tuominen VJ, Isola J, Valjakka J, Pastorekova S, Pastorek J, Parkkila S
Characterization of non-specific cytotoxic cell receptor protein 1: a new member of the lectin-type subfamily of F-box proteins.
PLoS One 2011 ;6(11)e27152
PMID

Virtanen S, Alarmo EL, Sandström S, Ampuja M, Kallioniemi A
Bone morphogenetic protein -4 and -5 in pancreatic cancer--novel bidirectional players.
Exp Cell Res 2011 ;317(15)2136-46
PMID

Pelttari LM, Heikkinen T, Thompson D, Kallioniemi A, Schleutker J, Holli K, Blomqvist C, Aittomäki K, Bützow R, Nevanlinna H
RAD51C is a susceptibility gene for ovarian cancer.
Hum Mol Genet 2011 ;20(16)3278-88
PMID

Kuuselo R, Savinainen K, Sandström S, Autio R, Kallioniemi A
MED29, a component of the mediator complex, possesses both oncogenic and tumor suppressive characteristics in pancreatic cancer.
Int J Cancer 2011 ;129(11)2553-65
PMID

Kallioniemi A
DNA copy number analysis on tissue microarrays.
Methods Mol Biol 2010 ;664127-34
PMID

Wolf M, Korja M, Karhu R, Edgren H, Kilpinen S, Ojala K, Mousses S, Kallioniemi A, Haapasalo H
Array-based gene expression, CGH and tissue data defines a 12q24 gain in neuroblastic tumors with prognostic implication.
BMC Cancer 2010 ;10181
PMID

Alarmo EL, Kallioniemi A
Bone morphogenetic proteins in breast cancer: dual role in tumourigenesis?
Endocr Relat Cancer 2010 ;17(2)R123-39
PMID

Kuuselo R, Simon R, Karhu R, Tennstedt P, Marx AH, Izbicki JR, Yekebas E, Sauter G, Kallioniemi A
19q13 amplification is associated with high grade and stage in pancreatic cancer.
Genes Chromosomes Cancer 2010 ;49(6)569-75
PMID

Ketolainen JM, Alarmo EL, Tuominen VJ, Kallioniemi A
Parallel inhibition of cell growth and induction of cell migration and invasion in breast cancer cells by bone morphogenetic protein 4.
Breast Cancer Res Treat 2010 ;124(2)377-86
PMID

Laurila E, Savinainen K, Kuuselo R, Karhu R, Kallioniemi A
Characterization of the 7q21-q22 amplicon identifies ARPC1A, a subunit of the Arp2/3 complex, as a regulator of cell migration and invasion in pancreatic cancer.
Genes Chromosomes Cancer 2009 ;48(4)330-9
PMID

Alarmo EL, Pärssinen J, Ketolainen JM, Savinainen K, Karhu R, Kallioniemi A
BMP7 influences proliferation, migration, and invasion of breast cancer cells.
Cancer Lett 2009 ;275(1)35-43
PMID

Heinonen H, Nieminen A, Saarela M, Kallioniemi A, Klefström J, Hautaniemi S, Monni O
Deciphering downstream gene targets of PI3K/mTOR/p70S6K pathway in breast cancer.
BMC Genomics 2008 ;9348
PMID

Erkko H, Dowty JG, Nikkilä J, Syrjäkoski K, Mannermaa A, Pylkäs K, Southey MC, Holli K, Kallioniemi A, Jukkola-Vuorinen A, Kataja V, Kosma VM, Xia B, Livingston DM, Winqvist R, Hopper JL
Penetrance analysis of the PALB2 c.1592delT founder mutation.
Clin Cancer Res 2008 ;14(14)4667-71
PMID

Fagerholm R, Hofstetter B, Tommiska J, Aaltonen K, Vrtel R, Syrjäkoski K, Kallioniemi A, Kilpivaara O, Mannermaa A, Kosma VM, Uusitupa M, Eskelinen M, Kataja V, Aittomäki K, von Smitten K, Heikkilä P, Lukas J, Holli K, Bartkova J, Blomqvist C, Bartek J, Nevanlinna H
NAD(P)H:quinone oxidoreductase 1 NQO1*2 genotype (P187S) is a strong prognostic and predictive factor in breast cancer.
Nat Genet 2008 ;40(7)844-53
PMID

Lind GE, Ahlquist T, Kolberg M, Berg M, Eknaes M, Alonso MA, Kallioniemi A, Meling GI, Skotheim RI, Rognum TO, Thiis-Evensen E, Lothe RA
Hypermethylated MAL gene - a silent marker of early colon tumorigenesis.
J Transl Med 2008 ;613
PMID

Pärssinen J, Alarmo EL, Karhu R, Kallioniemi A
PPM1D silencing by RNA interference inhibits proliferation and induces apoptosis in breast cancer cell lines with wild-type p53.
Cancer Genet Cytogenet 2008 ;182(1)33-9
PMID

Kallioniemi A
CGH microarrays and cancer.
Curr Opin Biotechnol 2008 ;19(1)36-40
PMID

Pärssinen J, Alarmo EL, Khan S, Karhu R, Vihinen M, Kallioniemi A
Identification of differentially expressed genes after PPM1D silencing in breast cancer.
Cancer Lett 2008 ;259(1)61-70
PMID

Kuuselo R, Savinainen K, Azorsa DO, Basu GD, Karhu R, Tuzmen S, Mousses S, Kallioniemi A
Intersex-like (IXL) is a cell survival regulator in pancreatic cancer with 19q13 amplification.
Cancer Res 2007 ;67(5)1943-9
PMID

Erkko H, Xia B, Nikkilä J, Schleutker J, Syrjäkoski K, Mannermaa A, Kallioniemi A, Pylkäs K, Karppinen SM, Rapakko K, Miron A, Sheng Q, Li G, Mattila H, Bell DW, Haber DA, Grip M, Reiman M, Jukkola-Vuorinen A, Mustonen A, Kere J, Aaltonen LA, Kosma VM, Kataja V, Soini Y, Drapkin RI, Livingston DM, Winqvist R
A recurrent mutation in PALB2 in Finnish cancer families.
Nature 2007 ;446(7133)316-9
PMID

Syrjäkoski K, Jäntti J, Kallioniemi A, Karhu R
Mutations in the BRCA2 interacting DSS1 are not a risk factor for male breast cancer.
Int J Cancer 2007 ;120(2)444-6
PMID

Alarmo EL, Kuukasjärvi T, Karhu R, Kallioniemi A
A comprehensive expression survey of bone morphogenetic proteins in breast cancer highlights the importance of BMP4 and BMP7.
Breast Cancer Res Treat 2007 ;103(2)239-46
PMID

Karhu R, Laurila E, Kallioniemi A, Syrjäkoski K
Large genomic BRCA2 rearrangements and male breast cancer.
Cancer Detect Prev 2006 ;30(6)530-4
PMID

Karhu R, Mahlamäki E, Kallioniemi A
Pancreatic adenocarcinoma -- genetic portrait from chromosomes to microarrays.
Genes Chromosomes Cancer 2006 ;45(8)721-30
PMID

Alarmo EL, Rauta J, Kauraniemi P, Karhu R, Kuukasjärvi T, Kallioniemi A
Bone morphogenetic protein 7 is widely overexpressed in primary breast cancer.
Genes Chromosomes Cancer 2006 ;45(4)411-9
PMID

Rauta J, Alarmo EL, Kauraniemi P, Karhu R, Kuukasjärvi T, Kallioniemi A
The serine-threonine protein phosphatase PPM1D is frequently activated through amplification in aggressive primary breast tumours.
Breast Cancer Res Treat 2006 ;95(3)257-63
PMID

Laurila E, Syrjäkoski K, Holli K, Kallioniemi A, Karhu R
Search for large genomic alterations of the BRCA1 gene in a Finnish population.
Cancer Genet Cytogenet 2005 ;163(1)57-61
PMID

Honrado E, Osorio A, Palacios J, Milne RL, Sánchez L, Díez O, Cazorla A, Syrjakoski K, Huntsman D, Heikkilä P, Lerma E, Kallioniemi A, Rivas C, Foulkes WD, Nevanlinna H, Benítez J
Immunohistochemical expression of DNA repair proteins in familial breast cancer differentiate BRCA2-associated tumors.
J Clin Oncol 2005 ;23(30)7503-11
PMID

Wikman H, Nymark P, Väyrynen A, Jarmalaite S, Kallioniemi A, Salmenkivi K, Vainio-Siukola K, Husgafvel-Pursiainen K, Knuutila S, Wolf M, Anttila S
CDK4 is a probable target gene in a novel amplicon at 12q13.3-q14.1 in lung cancer.
Genes Chromosomes Cancer 2005 ;42(2)193-9
PMID

Bärlund M, Kuukasjärvi T, Syrjäkoski K, Auvinen A, Kallioniemi A
Frequent amplification and overexpression of CCND1 in male breast cancer.
Int J Cancer 2004 ;111(6)968-71
PMID

Kauraniemi P, Hautaniemi S, Autio R, Astola J, Monni O, Elkahloun A, Kallioniemi A
Effects of Herceptin treatment on global gene expression patterns in HER2-amplified and nonamplified breast cancer cell lines.
Oncogene 2004 ;23(4)1010-3
PMID

Autio R, Hautaniemi S, Kauraniemi P, Yli-Harja O, Astola J, Wolf M, Kallioniemi A
CGH-Plotter: MATLAB toolbox for CGH-data analysis.
Bioinformatics 2003 ;19(13)1714-5
PMID

Skotheim RI, Kallioniemi A, Bjerkhagen B, Mertens F, Brekke HR, Monni O, Mousses S, Mandahl N, Soeter G, Nesland JM, Smeland S, Kallioniemi OP, Lothe RA
Topoisomerase-II alpha is upregulated in malignant peripheral nerve sheath tumors and associated with clinical outcome.
J Clin Oncol 2003 ;21(24)4586-91
PMID

Kauraniemi P, Kuukasjärvi T, Sauter G, Kallioniemi A
Amplification of a 280-kilobase core region at the ERBB2 locus leads to activation of two hypothetical proteins in breast cancer.
Am J Pathol 2003 ;163(5)1979-84
PMID

Kallioniemi A
[Gene expression profile as a crystal ball].
Duodecim 2003 ;119(12)1101-2
PMID

Kallioniemi A
Molecular signatures of breast cancer--predicting the future.
N Engl J Med 2002 ;347(25)2067-8
PMID

Hyman E, Kauraniemi P, Hautaniemi S, Wolf M, Mousses S, Rozenblum E, Ringnér M, Sauter G, Monni O, Elkahloun A, Kallioniemi OP, Kallioniemi A
Impact of DNA amplification on gene expression patterns in breast cancer.
Cancer Res 2002 ;62(21)6240-5
PMID

Mahlamäki EH, Bärlund M, Tanner M, Gorunova L, Höglund M, Karhu R, Kallioniemi A
Frequent amplification of 8q24, 11q, 17q, and 20q-specific genes in pancreatic cancer.
Genes Chromosomes Cancer 2002 ;35(4)353-8
PMID

Bärlund M, Monni O, Weaver JD, Kauraniemi P, Sauter G, Heiskanen M, Kallioniemi OP, Kallioniemi A
Cloning of BCAS3 (17q23) and BCAS4 (20q13) genes that undergo amplification, overexpression, and fusion in breast cancer.
Genes Chromosomes Cancer 2002 ;35(4)311-7
PMID

Andersen CL, Monni O, Wagner U, Kononen J, Bärlund M, Bucher C, Haas P, Nocito A, Bissig H, Sauter G, Kallioniemi A
High-throughput copy number analysis of 17q23 in 3520 tissue specimens by fluorescence in situ hybridization to tissue microarrays.
Am J Pathol 2002 ;161(1)73-9
PMID

Bulavin DV, Demidov ON, Saito S, Kauraniemi P, Phillips C, Amundson SA, Ambrosino C, Sauter G, Nebreda AR, Anderson CW, Kallioniemi A, Fornace AJ, Appella E
Amplification of PPM1D in human tumors abrogates p53 tumor-suppressor activity.
Nat Genet 2002 ;31(2)210-5
PMID

Varis A, Wolf M, Monni O, Vakkari ML, Kokkola A, Moskaluk C, Frierson H, Powell SM, Knuutila S, Kallioniemi A, El-Rifai W
Targets of gene amplification and overexpression at 17q in gastric cancer.
Cancer Res 2002 ;62(9)2625-9
PMID

Skotheim RI, Monni O, Mousses S, Fosså SD, Kallioniemi OP, Lothe RA, Kallioniemi A
New insights into testicular germ cell tumorigenesis from gene expression profiling.
Cancer Res 2002 ;62(8)2359-64
PMID

Mousses S, Kallioniemi A, Kauraniemi P, Elkahloun A, Kallioniemi OP
Clinical and functional target validation using tissue and cell microarrays.
Curr Opin Chem Biol 2002 ;6(1)97-101
PMID

 
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