Tissue Profiling

SciLifeLab Infrastructure Unit 2013–2018.

Started: 2013

Ended: 2018

178 publications

Year 2017

Breast cancer in young women and prognosis: How important are proliferation markers?
Fredholm H, Magnusson K, Lindström LS, ..., Frisell J, Fredriksson I
pii: S0959-8049(17)31177-2
Eur. J. Cancer 84 (-) 278-289 [2017-10-00; online 2017-08-29]
Tissue Profiling [Collaborative]
Tumoral cubilin is a predictive marker for treatment of renal cancer patients with sunitinib and sorafenib.
Niinivirta M, Enblad G, Edqvist PH, ..., Dragomir A, Ullenhag GJ
pii: 10.1007/s00432-017-2365-y pmc: PMC5427164
J. Cancer Res. Clin. Oncol. 143 (6) 961-970 [2017-06-00; online 2017-03-04]
Tissue Profiling [Collaborative]
Associations of defect mismatch repair genes with prognosis and heredity in sporadic colorectal cancer.
Ghanipour L, Jirström K, Sundström M, Glimelius B, Birgisson H
pii: S0748-7983(16)30951-9
Eur J Surg Oncol 43 (2) 311-321 [2017-02-00; online 2016-11-12]
Tissue Profiling [Service]
Perivascular PDGFR-β is an independent marker for prognosis in renal cell carcinoma.
Frödin M, Mezheyeuski A, Corvigno S, ..., Johansson M, Östman A
pii: bjc2016407 pmc: PMC5243993
Br. J. Cancer 116 (2) 195-201 [2017-01-17; online 2016-12-09]
Tissue Profiling [Service]
A systematic search strategy identifies cubilin as independent prognostic marker for renal cell carcinoma.
Gremel G, Djureinovic D, Niinivirta M, ..., Stewart GD, Pontén F
pii: 10.1186/s12885-016-3030-6 pmc: PMC5215231
BMC Cancer 17 (1) 9 [2017-01-04; online 2017-01-04]
Tissue Profiling [Technology development]

Year 2016

The protein phosphatase 2A regulatory subunit PR70 is a gonosomal melanoma tumor suppressor gene.
van Kempen LC, Redpath M, Elchebly M, ..., Feunteun J, Spatz A
pii: 8/369/369ra177
Sci Transl Med 8 (369) 369ra177 [2016-12-14; online 2016-12-16]
Tissue Profiling [Collaborative]
Looking for Missing Proteins in the Proteome of Human Spermatozoa: An Update.
Vandenbrouck Y, Lane L, Carapito C, ..., Garin J, Pineau C
J. Proteome Res. 15 (11) 3998-4019 [2016-11-04; online 2016-08-23]
Tissue Profiling [Collaborative]
Long-term outcome in young women with breast cancer: a population-based study.
Fredholm H, Magnusson K, Lindström LS, ..., Frisell J, Fredriksson I
pii: 10.1007/s10549-016-3983-9 pmc: PMC5050247
Breast Cancer Res. Treat. 160 (1) 131-143 [2016-11-00; online 2016-09-13]
Tissue Profiling [Collaborative]
Gene‐specific correlation of RNA and protein levels in human cells and tissues
Edfors F, Danielsson F, Hallström BM, ..., Forsström B, Uhlén M
Mol. Syst. Biol. 12 (10) 883 [2016-10-00; online 2016-10-20]
Tissue Profiling [Collaborative]
Analysis of Body-wide Unfractionated Tissue Data to Identify a Core Human Endothelial Transcriptome.
Butler LM, Hallström BM, Fagerberg L, ..., Renné T, Odeberg J
pii: S2405-4712(16)30256-3
Cell Syst 3 (3) 287-301.e3 [2016-09-28; online 2016-09-15]
Tissue Profiling [Collaborative]
Tissue microarray profiling in human heart failure.
Lal S, Nguyen L, Tezone R, ..., Li A, Dos Remedios C
Proteomics 16 (17) 2319-2326 [2016-09-00; online 2016-08-11]
Tissue Profiling [Collaborative]
Inconsistent results in the analysis of ALK rearrangements in non-small cell lung cancer.
Mattsson JS, Brunnström H, Jabs V, ..., Micke P, Svensson MA
pii: 10.1186/s12885-016-2646-x pmc: PMC4974795
BMC Cancer 16 (-) 603 [2016-08-05; online 2016-08-05]
Tissue Profiling [Collaborative]
SATB2 is expressed in Merkel cell carcinoma.
Fukuhara M, Agnarsdóttir M, Edqvist PH, Coter A, Ponten F
pii: 10.1007/s00403-016-1655-6
Arch. Dermatol. Res. 308 (6) 449-454 [2016-08-00; online 2016-06-04]
Tissue Profiling [Technology development]
Guidance Molecule SEMA3A Restricts Tumor Growth by Differentially Regulating the Proliferation of Tumor-Associated Macrophages.
Wallerius M, Wallmann T, Bartish M, ..., Andersson J, Rolny C
pii: 0008-5472.CAN-15-2596
Cancer Res. 76 (11) 3166-3178 [2016-06-01; online 2016-04-06]
Tissue Profiling [Collaborative]
System-wide Clinical Proteomics of Breast Cancer Reveals Global Remodeling of Tissue Homeostasis.
Pozniak Y, Balint-Lahat N, Rudolph JD, ..., Barshack I, Geiger T
pii: S2405-4712(16)30031-X
Cell Syst 2 (3) 172-184 [2016-03-23; online 2016-03-03]
Tissue Profiling [Collaborative]
Oncogene-Induced Senescence in Pituitary Adenomas--an Immunohistochemical Study.
Manojlovic-Gacic E, Skender-Gazibara M, Popovic V, ..., Pontén F, Casar-Borota O
pii: 10.1007/s12022-015-9405-4
Endocr. Pathol. 27 (1) 1-11 [2016-03-00; online 2015-11-18]
Tissue Profiling [Collaborative]

Year 2015

High levels of WNT-5A in human glioma correlate with increased presence of tumor-associated microglia/monocytes.
Dijksterhuis JP, Arthofer E, Marinescu VD, ..., Mulder J, Schulte G
pii: S0014-4827(15)30133-6
Exp. Cell Res. 339 (2) 280-288 [2015-12-10; online 2015-10-25]
Tissue Profiling [Collaborative]
Emmprin Expression Predicts Response and Survival following Cisplatin Containing Chemotherapy for Bladder Cancer: A Validation Study.
Hemdan T, Malmström PU, Jahnson S, Segersten U
pii: S0022-5347(15)04296-2
J. Urol. 194 (6) 1575-1581 [2015-12-00; online 2015-06-30]
Tissue Profiling
Foxf2 Is Required for Brain Pericyte Differentiation and Development and Maintenance of the Blood-Brain Barrier.
Reyahi A, Nik AM, Ghiami M, ..., Johansson BR, Carlsson P
pii: S1534-5807(15)00324-X
Dev. Cell 34 (1) 19-32 [2015-07-06; online 2015-06-25]
Tissue Profiling [Collaborative]
Loss of ASRGL1 expression is an independent biomarker for disease-specific survival in endometrioid endometrial carcinoma.
Edqvist PH, Huvila J, Forsström B, ..., Pontén F, Auranen A
pii: S0090-8258(15)00783-0
Gynecol. Oncol. 137 (3) 529-537 [2015-06-00; online 2015-04-07]
Tissue Profiling [Collaborative]
Prognostic impact of COX-2 in non-small cell lung cancer: a comprehensive compartment-specific evaluation of tumor and stromal cell expression.
Mattsson JS, Bergman B, Grinberg M, ..., Micke P, Gulyas M
pii: S0304-3835(14)00631-4
Cancer Lett. 356 (2 Pt B) 837-845 [2015-01-28; online 2014-10-31]
Tissue Profiling [Collaborative]

Year 2014

Aberrantly activated claudin 6 and 18.2 as potential therapy targets in non-small-cell lung cancer.
Micke P, Mattsson JS, Edlund K, ..., Sahin U, Türeci O
Int. J. Cancer 135 (9) 2206-2214 [2014-11-01; online 2014-04-09]
Tissue Profiling
Histidine-rich glycoprotein uptake and turnover is mediated by mononuclear phagocytes.
Tugues S, Roche F, Noguer O, ..., Tolmachev V, Claesson-Welsh L
pii: PONE-D-14-06030 pmc: PMC4171488
PLoS ONE 9 (9) e107483 [2014-09-22; online 2014-09-22]
Tissue Profiling
The prognostic value and therapeutic target role of stathmin-1 in urinary bladder cancer.
Hemdan T, Lindén M, Lind SB, ..., Malmström PU, Segersten U
pii: bjc2014427 pmc: PMC4453855
Br. J. Cancer 111 (6) 1180-1187 [2014-09-09; online 2014-07-29]
Tissue Profiling [Collaborative]
An integrative analysis of the tumorigenic role of TAZ in human non-small cell lung cancer.
Noguchi S, Saito A, Horie M, ..., Micke P, Nagase T
pii: 1078-0432.CCR-13-3328
Clin. Cancer Res. 20 (17) 4660-4672 [2014-09-01; online 2014-06-22]
Tissue Profiling
Analysis of candidate genes for lineage-specific expression changes in humans and primates.
Lindskog C, Kuhlwilm M, Davierwala A, ..., Pääbo S, Pontén F
J. Proteome Res. 13 (8) 3596-3606 [2014-08-01; online 2014-06-10]
Tissue Profiling
Decreased decorin expression in the tumor microenvironment.
Bozoky B, Savchenko A, Guven H, ..., Klein G, Szekely L
Cancer Med 3 (3) 485-491 [2014-06-00; online 2014-03-19]
Tissue Profiling
Garbage in, garbage out: a critical evaluation of strategies used for validation of immunohistochemical biomarkers.
O'Hurley G, Sjöstedt E, Rahman A, ..., Gallagher WM, Lindskog C
pii: S1574-7891(14)00056-8
Mol Oncol 8 (4) 783-798 [2014-06-00; online 2014-04-15]
Tissue Profiling
WNT5A-mediated β-catenin-independent signalling is a novel regulator of cancer cell metabolism.
Sherwood V, Chaurasiya SK, Ekström EJ, ..., James P, Andersson T
pii: bgt390 pmc: PMC3977146
Carcinogenesis 35 (4) 784-794 [2014-04-00; online 2013-12-03]
Tissue Profiling
Investigation of molecular alterations of AKT-3 in triple-negative breast cancer.
O'Hurley G, Daly E, O'Grady A, ..., Kay EW, Gallagher WM
Histopathology 64 (5) 660-670 [2014-04-00; online 2013-10-22]
Tissue Profiling
Antibody performance in western blot applications is context-dependent.
Algenäs C, Agaton C, Fagerberg L, ..., Ottosson Takanen J, Hober S
Biotechnol J 9 (3) 435-445 [2014-03-00; online 2014-01-10]
Cell Profiling Tissue Profiling
Subtyping of gliomas of various WHO grades by the application of immunohistochemistry.
Popova SN, Bergqvist M, Dimberg A, ..., Sooman L, Alafuzoff I
Histopathology 64 (3) 365-379 [2014-02-00; online 2014-01-15]
Tissue Profiling
Glioma-derived macrophage migration inhibitory factor (MIF) promotes mast cell recruitment in a STAT5-dependent manner.
Põlajeva J, Bergström T, Edqvist PH, ..., Forsberg Nilsson K, Tchougounova E
pii: S1574-7891(13)00137-3
Mol Oncol 8 (1) 50-58 [2014-02-00; online 2013-10-05]
Tissue Profiling
Genome-scale metabolic modelling of hepatocytes reveals serine deficiency in patients with non-alcoholic fatty liver disease.
Mardinoglu A, Agren R, Kampf C, ..., Uhlen M, Nielsen J
pii: ncomms4083
Nat Commun 5 (-) 3083 [2014-01-15; online 2014-01-15]
Tissue Profiling
A systematic analysis of commonly used antibodies in cancer diagnostics.
Gremel G, Bergman J, Djureinovic D, ..., Micke P, Pontén F
Histopathology 64 (2) 293-305 [2014-01-00; online 2013-12-18]
Tissue Profiling

Year 2013

Antibodies biotinylated using a synthetic Z-domain from protein A provide stringent in situ protein detection.
Andersson S, Konrad A, Ashok N, ..., Hober S, Asplund A
pii: 0022155413502360 pmc: PMC3808578
J. Histochem. Cytochem. 61 (11) 773-784 [2013-11-00; online 2013-08-08]
Tissue Profiling
In situ Protein Detection for Companion Diagnostics.
Gremel G, Grannas K, Sutton LA, Pontén F, Zieba A
Front Oncol 3 (-) 271 [2013-10-31; online 2013-10-31]
Tissue Profiling
Heart research advances using database search engines, Human Protein Atlas and the Sydney Heart Bank.
Li A, Estigoy C, Raftery M, ..., Lal S, Dos Remedios CG
pii: S1443-9506(13)01036-6
Heart Lung Circ 22 (10) 819-826 [2013-10-00; online 2013-07-17]
Tissue Profiling
FHOD1, a formin upregulated in epithelial-mesenchymal transition, participates in cancer cell migration and invasion.
Gardberg M, Kaipio K, Lehtinen L, ..., Koivisto M, Carpén O
pii: PONE-D-13-15073 pmc: PMC3784416
PLoS ONE 8 (9) e74923 [2013-09-26; online 2013-09-26]
Tissue Profiling
Progesterone receptor negativity is an independent risk factor for relapse in patients with early stage endometrioid endometrial adenocarcinoma.
Huvila J, Talve L, Carpén O, ..., Grénman S, Auranen A
pii: S0090-8258(13)00848-2
Gynecol. Oncol. 130 (3) 463-469 [2013-09-00; online 2013-06-20]
Tissue Profiling
Tumour expression of bladder cancer-associated urinary proteins.
Lindén M, Segersten U, Runeson M, ..., Lind SB, Malmström PU
BJU Int. 112 (3) 407-415 [2013-08-00; online 2013-03-09]
Tissue Profiling
Novel signatures of cancer-associated fibroblasts.
Bozóky B, Savchenko A, Csermely P, ..., Székely L, Klein G
Int. J. Cancer 133 (2) 286-293 [2013-07-15; online 2013-01-16]
Tissue Profiling
Estrogen receptor β expression induces changes in the microRNA pool in human colon cancer cells.
Edvardsson K, Nguyen-Vu T, Kalasekar SM, ..., Gustafsson JÅ, Williams C
pii: bgt067
Carcinogenesis 34 (7) 1431-1441 [2013-07-00; online 2013-02-26]
Tissue Profiling
Initial quantitative proteomic map of 28 mouse tissues using the SILAC mouse.
Geiger T, Velic A, Macek B, ..., Cox J, Mann M
pii: M112.024919 pmc: PMC3675825
Mol. Cell Proteomics 12 (6) 1709-1722 [2013-06-00; online 2013-02-26]
Cell Profiling Tissue Profiling
European H16N3 gull influenza virus attaches to the human respiratory tract and eye.
Lindskog C, Ellström P, Olsen B, ..., Kuiken T, Jourdain E
pii: PONE-D-12-38518 pmc: PMC3620227
PLoS ONE 8 (4) e60757 [2013-04-08; online 2013-04-08]
Tissue Profiling
Integration of clinical data with a genome-scale metabolic model of the human adipocyte.
Mardinoglu A, Agren R, Kampf C, ..., Uhlen M, Nielsen J
pii: msb20135 pmc: PMC3619940
Mol. Syst. Biol. 9 (-) 649 [2013-03-21; online 2013-03-21]
Tissue Profiling
STC1 expression by cancer-associated fibroblasts drives metastasis of colorectal cancer.
Peña C, Céspedes MV, Lindh MB, ..., Augsten M, Ostman A
pii: 0008-5472.CAN-12-1875
Cancer Res. 73 (4) 1287-1297 [2013-02-15; online 2012-12-18]
Tissue Profiling

Year 2012

Transcription factor PROX1: its role in development and cancer.
Elsir T, Smits A, Lindström MS, Nistér M
Cancer Metastasis Rev. 31 (3-4) 793-805 [2012-12-00; online 2012-06-27]
Tissue Profiling
TPX2 and AURKA promote 20q amplicon-driven colorectal adenoma to carcinoma progression.
Sillars-Hardebol AH, Carvalho B, Tijssen M, ..., Fijneman RJ, Meijer GA
pii: gutjnl-2011-301153
Gut 61 (11) 1568-1575 [2012-11-00; online 2011-12-31]
Tissue Profiling
Consistent mutation status within histologically heterogeneous lung cancer lesions.
Mattsson JS, Imgenberg-Kreuz J, Edlund K, Botling J, Micke P
Histopathology 61 (4) 744-748 [2012-10-00; online 2012-03-31]
Tissue Profiling
A tool to facilitate clinical biomarker studies--a tissue dictionary based on the Human Protein Atlas.
Kampf C, Bergman J, Oksvold P, ..., Uhlén M, Ponten F
pii: 1741-7015-10-103 pmc: PMC3523031
BMC Med 10 (-) 103 [2012-09-12; online 2012-09-12]
Cell Profiling Tissue Profiling
Platelet-derived growth factor over-expression in retinal progenitors results in abnormal retinal vessel formation.
Edqvist PH, Niklasson M, Vidal-Sanz M, Hallböök F, Forsberg-Nilsson K
pii: PONE-D-11-21303 pmc: PMC3411765
PLoS ONE 7 (8) e42488 [2012-08-03; online 2012-08-03]
Tissue Profiling
GABA-A channel subunit expression in human glioma correlates with tumor histology and clinical outcome.
Smits A, Jin Z, Elsir T, ..., Aronica E, Birnir B
pii: PONE-D-12-03413 pmc: PMC3355166
PLoS ONE 7 (5) e37041 [2012-05-17; online 2012-05-17]
Tissue Profiling
Novel pancreatic beta cell-specific proteins: antibody-based proteomics for identification of new biomarker candidates.
Lindskog C, Korsgren O, Pontén F, ..., Johansson L, Danielsson A
pii: S1874-3919(12)00141-8
J Proteomics 75 (9) 2611-2620 [2012-05-17; online 2012-04-03]
Tissue Profiling
Scalable in situ hybridization on tissue arrays for validation of novel cancer and tissue-specific biomarkers.
Kiflemariam S, Andersson S, Asplund A, Pontén F, Sjöblom T
pii: PONE-D-11-18464 pmc: PMC3297615
PLoS ONE 7 (3) e32927 [2012-03-08; online 2012-03-08]
Tissue Profiling
Antibody-based protein profiling of the human chromosome 21.
Uhlén M, Oksvold P, Älgenäs C, ..., Kondo T, Sivertsson Å
pii: M111.013458 pmc: PMC3316724
Mol. Cell Proteomics 11 (3) M111.013458 [2012-03-00; online 2011-11-02]
Cell Profiling Tissue Profiling
BCL2L1 has a functional role in colorectal cancer and its protein expression is associated with chromosome 20q gain.
Sillars-Hardebol AH, Carvalho B, Beliën JA, ..., Fijneman RJ, Meijer GA
J. Pathol. 226 (3) 442-450 [2012-02-00; online 2011-10-20]
Tissue Profiling

Year 2011

High nuclear RBM3 expression is associated with an improved prognosis in colorectal cancer.
Hjelm B, Brennan DJ, Zendehrokh N, ..., Jirström K, Uhlen M
Proteomics Clin Appl 5 (11-12) 624-635 [2011-12-00; online 2011-10-01]
Tissue Profiling
Large-scale protein profiling in human cell lines using antibody-based proteomics.
Fagerberg L, Strömberg S, El-Obeid A, ..., Ponten F, Asplund A
J. Proteome Res. 10 (9) 4066-4075 [2011-09-02; online 2011-07-06]
Tissue Profiling
Functional and prognostic relevance of the homeobox protein MSX2 in malignant melanoma.
Gremel G, Ryan D, Rafferty M, ..., Ponten F, Gallagher WM
pii: bjc2011249 pmc: PMC3170959
Br. J. Cancer 105 (4) 565-574 [2011-08-09; online 2011-07-07]
Tissue Profiling
RBM3-regulated genes promote DNA integrity and affect clinical outcome in epithelial ovarian cancer.
Ehlén Å, Nodin B, Rexhepaj E, ..., Brennan DJ, Jirström K
Transl Oncol 4 (4) 212-221 [2011-08-00; online 2011-08-01]
Tissue Profiling
SATB2 in combination with cytokeratin 20 identifies over 95% of all colorectal carcinomas.
Magnusson K, de Wit M, Brennan DJ, ..., Jirström K, Pontén F
pii: 00000478-201107000-00001
Am. J. Surg. Pathol. 35 (7) 937-948 [2011-07-00; online 2011-06-17]
Cell Profiling Tissue Profiling
Growth differentiation factor 15: a prognostic marker for recurrence in colorectal cancer.
Wallin U, Glimelius B, Jirström K, ..., Påhlman L, Birgisson H
pii: bjc2011112 pmc: PMC3101900
Br. J. Cancer 104 (10) 1619-1627 [2011-05-10; online 2011-04-07]
Tissue Profiling
Diagnostic biomarkers of prostate cancer.
Häggarth L, Hägglöf C, Jaraj SJ, ..., Ostman A, Egevad L
Scand. J. Urol. Nephrol. 45 (1) 60-67 [2011-02-00; online 2010-11-03]
Tissue Profiling
GAD1 is a biomarker for benign and malignant prostatic tissue.
Jaraj SJ, Augsten M, Häggarth L, ..., Ostman A, Egevad L
Scand. J. Urol. Nephrol. 45 (1) 39-45 [2011-02-00; online 2010-11-26]
Tissue Profiling
HRG inhibits tumor growth and metastasis by inducing macrophage polarization and vessel normalization through downregulation of PlGF.
Rolny C, Mazzone M, Tugues S, ..., Claesson-Welsh L, Carmeliet P
pii: S1535-6108(10)00474-5
Cancer Cell 19 (1) 31-44 [2011-01-18; online 2011-01-11]
Tissue Profiling

Year 2010

SOX10 expression in superficial spreading and nodular malignant melanomas.
Agnarsdóttir M, Sooman L, Bolander A, ..., Uhlen M, Hedstrand H
Melanoma Res. 20 (6) 468-478 [2010-12-00; online 2010-10-05]
Tissue Profiling
Topoisomerase I amplification in melanoma is associated with more advanced tumours and poor prognosis.
Ryan D, Rafferty M, Hegarty S, ..., Dervan PA, Gallagher WM
pii: PCR720
Pigment Cell Melanoma Res 23 (4) 542-553 [2010-08-00; online 2010-05-15]
Tissue Profiling
Antibody-based proteomics for discovery and exploration of proteins expressed in pancreatic islets.
Lindskog C, Asplund A, Engkvist M, ..., Korsgren O, Ponten F
Discov Med 9 (49) 565-578 [2010-06-00; online 2010-07-01]
Tissue Profiling
Tumour-specific HMG-CoAR is an independent predictor of recurrence free survival in epithelial ovarian cancer.
Brennan DJ, Brändstedt J, Rexhepaj E, ..., O'Herlihy C, Jirstrom K
pii: 1471-2407-10-125 pmc: PMC3087316
BMC Cancer 10 (-) 125 [2010-04-01; online 2010-04-01]
Tissue Profiling
The impact of tissue fixatives on morphology and antibody-based protein profiling in tissues and cells.
Paavilainen L, Edvinsson A, Asplund A, ..., Pontén F, Wester K
pii: jhc.2009.954321 pmc: PMC2825489
J. Histochem. Cytochem. 58 (3) 237-246 [2010-03-00; online 2009-11-11]
Tissue Profiling
Tissue-Specific Protein Expression in Human Cells, Tissues and Organs
Gry M, Oksvold P, Pontén F, Uhlén M
JPB 03 (10) - [2010-00-00; online 2010-00-00]
Tissue Profiling