BEA - reference list

2024

Mechanical loading intensities affect the release of extracellular vesicles from mouse bone marrow-derived hematopoietic progenitor cells and change their osteoclast-modulating effect.
Bratengeier C, Johansson L, Liszka A, Bakker AD, Hallbeck M, Fahlgren A
FASEB J 2024 Jan;38(1):e23323

Decreased mitochondrial-related gene expression in adipose tissue after acute sprint exercise in humans: A pilot study.
Esbjörnsson M, Rundqvist HC, Norman B, Österlund T, Rullman E, Bülow J, Jansson E
Physiol Rep 2024 Oct;12(20):e70088

Sustained immune activation and impaired epithelial barrier integrity in the ectocervix of women with chronic HIV infection.
Franzén Boger M, Hasselrot T, Kaldhusdal V, Miranda GHB, Czarnewski P, Edfeldt G, Bradley F, Rexaj G, Lajoie J, Omollo K, Kimani J, Fowke KR, Broliden K, Tjernlund A
PLoS Pathog 2024 Nov;20(11):e1012709

Estradiol-mediated enhancement of the human ectocervical epithelial barrier correlates with desmoglein-1 expression in the follicular menstrual phase.
Bradley F, Stern A, Franzén Boger M, Mousavian Z, Dethlefsen O, Kaldhusdal V, Lajoie J, Omollo K, Bergström S, Månberg A, Nilsson P, Kimani J, Burgener AD, Tjernlund A, Sundling C, Fowke KR, Broliden K
Front Endocrinol (Lausanne) 2024 ;15():1454006

Effects of chemical in vitro activation versus fragmentation on human ovarian tissue and follicle growth in culture.
Hao J, Li T, Heinzelmann M, Moussaud-Lamodière E, Lebre F, Krjutškov K, Damdimopoulos A, Arnelo C, Pettersson K, Alfaro-Moreno E, Lindskog C, van Duursen M, Damdimopoulou P
Hum Reprod Open 2024 ;2024(3):hoae028

Jag1 insufficiency alters liver fibrosis via T cell and hepatocyte differentiation defects.
Mašek J, Filipovic I, Van Hul N, Belicová L, Jiroušková M, Oliveira DV, Frontino AM, Hankeova S, He J, Turetti F, Iqbal A, Červenka I, Sarnová L, Verboven E, Brabec T, Björkström NK, Gregor M, Dobeš J, Andersson ER
EMBO Mol Med 2024 Nov;16(11):2946-2975

Intravenous chaperone treatment of late-stage Alzheimer´s disease (AD) mouse model affects amyloid plaque load, reactive gliosis and AD-related genes.
Zhang R, Ohshima M, Brodin D, Wang Y, Morancé A, Schultzberg M, Chen G, Johansson J
Transl Psychiatry 2024 Oct;14(1):453

2023

Emerging role and clinical implication of mRNA scavenger decapping enzyme in colorectal cancer.
Jan Dimberg , Shamoun L, Johansson G, Landerholm K, Wågsäter D
Pathol Res Pract 2024 Jan;253():155009

Characterization of the bone marrow niche in patients with chronic myeloid leukemia identifies CXCL14 as a new therapeutic option.
Dolinska M, Cai H, Månsson A, Shen J, Xiao P, Bouderlique T, Li X, Leonard E, Chang M, Gao Y, Medina JP, Kondo M, Sandhow L, Johansson AS, Deneberg S, Söderlund S, Jädersten M, Ungerstedt J, Tobiasson M, Östman A, Mustjoki S, Stenke L, Le Blanc K, Hellström-Lindberg E, Lehmann S, Ekblom M, Olsson-Strömberg U, Sigvardsson M, Qian H
Blood 2023 Jul;142(1):73-89

TGFß1 Stimulates Lymphatic Endothelial Cells to Produce IL7 and IL15, Which Act as Chemotactic Factors for Breast Cancer Cells with Mesenchymal Properties.
Giotopoulou N, Shi W, Parniewska MM, Sun W, Fuxe J
J Mammary Gland Biol Neoplasia 2023 Dec;28(1):25

The single-cell transcriptional landscape of innate and adaptive lymphocytes in pediatric-onset colitis.
Kokkinou E, Soini T, Pandey RV, van Acker A, Theorell J, Czarnewski P, Kvedaraite E, Vandamme N, Lourda M, Sorini C, Weigel W, Carrasco A, Tibbitt CA, Schlums H, Lindforss U, Nordenvall C, Ljunggren M, Ideström M, Svensson M, Henter JI, Villablanca EJ, Bryceson YT, Rolandsdotter H, Mjösberg J
Cell Rep Med 2023 May;4(5):101038

Stem cell-derived brainstem mouse astrocytes obtain a neurotoxic phenotype in vitro upon neuroinflammation.
Lindblad C, Neumann S, Kolbeinsdóttir S, Zachariadis V, Thelin EP, Enge M, Thams S, Brundin L, Svensson M
J Inflamm (Lond) 2023 Jun;20(1):22

Irradiation and lithium treatment alter the global DNA methylation pattern and gene expression underlying a shift from gliogenesis towards neurogenesis in human neural progenitors.
Neofytou C, Backlund A, Blomgren K, Hermanson O
Transl Psychiatry 2023 Jul;13(1):258

Control of protein synthesis through mRNA pseudouridylation by dyskerin.
Pederiva C, Trevisan DM, Peirasmaki D, Chen S, Savage SA, Larsson O, Ule J, Baranello L, Agostini F, Farnebo M
Sci Adv 2023 Jul;9(30):eadg1805

Chemical Modifications and Design Influence the Potency of Huntingtin Anti-Gene Oligonucleotides.
Saher O, Zaghloul EM, Umek T, Hagey DW, Mozafari N, Danielsen MB, Gouda AS, Lundin KE, Jørgensen PT, Wengel J, Smith CIE, Zain R
Nucleic Acid Ther 2023 Apr;33(2):117-131

Skin mesenchymal niches maintain and protect AML-initiating stem cells.
Sandhow L, Cai H, Leonard E, Xiao P, Tomaipitinca L, Månsson A, Kondo M, Sun X, Johansson AS, Tryggvason K, Kasper M, Järås M, Qian H
J Exp Med 2023 Oct;220(10):

Global loss of cellular m6A RNA methylation following infection with different SARS-CoV-2 variants.
Vaid R, Mendez A, Thombare K, Burgos-Panadero R, Robinot R, Fonseca BF, Gandasi NR, Ringlander J, Hassan Baig M, Dong JJ, Cho JY, Reinius B, Chakrabarti LA, Nystrom K, Mondal T
Genome Res 2023 Mar;33(3):299-313

An essential role for the Ino80 chromatin remodeling complex in regulation of gene expression during cellular quiescence.
Zahedi Y, Zeng S, Ekwall K
Chromosome Res 2023 Apr;31(2):14

2022

The release of osteoclast-stimulating factors on supraphysiological loading by osteoprogenitors coincides with expression of genes associated with inflammation and cytoskeletal arrangement.
Bratengeier C, Bakker AD, Liszka A, Schilcher J, Fahlgren A
Sci Rep 2022 Dec;12(1):215782022

Plasma RNA profiling unveils transcriptional signatures associated with resistance to osimertinib in EGFR T790M positive non-small cell lung cancer patients.
Alexeyenko A, Brustugun OT, Eide IJZ, Gencheva R, Kosibaty Z, Lai Y, de Petris L, Tsakonas G, Grundberg O, Franzen B, Viktorsson K, Lewensohn R, Hydbring P, Ekman S
Transl Lung Cancer Res 2022 Oct;11(10):2064-2078

Critical role of Lama4 for hematopoiesis regeneration and acute myeloid leukemia progression.
Cai H, Kondo M, Sandhow L, Xiao P, Johansson AS, Sasaki T, Zawacka-Pankau J, Tryggvason K, Ungerstedt J, Walfridsson J, Ekblom M, Qian H
Blood 2022 May;139(20):3040-3057

Distinct T cell subsets in adipose tissue are associated with obesity.
Haugstøyl ME, Cornillet M, Strand K, Stiglund N, Sun D, Lawrence-Archer L, Hjellestad ID, Sparrelid E, Busch C, Hjelmesaeth J, Hertel JK, Ponzetta A, Mellgren G, Fernø J, Björkström NK
Eur J Immunol 2023 Feb;53(2):e2249990

Identification of GTF2IRD1 as a novel transcription factor essential for acute myeloid leukemia
Heshmati Y, Türköz G, Zawacka J.E,  Dimitriou M, Harisankar A, Boström J, Cai H, Kadri N,  Altun M, Qian H, Walfridsson J. (Preprint). https://doi.org/10.1101/2022.08.09.503300

Prolonged estrogen deprivation triggers a broad immunosuppressive phenotype in breast cancer cells.
Hühn D, Martí-Rodrigo P, Mouron S, Hansel C, Tschapalda K, Porebski B, Häggblad M, Lidemalm L, Quintela-Fandino M, Carreras-Puigvert J, Fernandez-Capetillo O
Mol Oncol 2022 Jan;16(1):148-165

Integrative small and long RNA omics analysis of human healing and nonhealing wounds discovers cooperating microRNAs as therapeutic targets.
Liu Z, Zhang L, Toma MA, Li D, Bian X, Pastar I, Tomic-Canic M, Sommar P, Xu Landén N
Elife 2022 Aug;11():

Omega-3 fatty acids decrease CRYAB, production of oncogenic prostaglandin E2 and suppress tumor growth in medulloblastoma.
Ljungblad L, Bergqvist F, Tümmler C, Madawala S, Olsen TK, Andonova T, Jakobsson PJ, Johnsen JI, Pickova J, Strandvik B, Kogner P, Gleissman H, Wickström M
Life Sci 2022 Apr;295():120394

Defining post-acute COVID-19 syndrome (PACS) by an epigenetic biosignature in peripheral blood mononuclear cells.
Nikesjö F, Sayyab S, Karlsson L, Apostolou E, Rosén A, Hedman K, Lerm M
Clin Epigenetics 2022 Dec;14(1):172

Altered mRNA Expression Due to Rectal Perforation in a Porcine Model - A Pilot Study.
Oikonomakis I, Brodin D, Hörer TM, Skoog P, Seilitz J, Nilsson KF, Meehan AD, Jansson K
Anticancer Res 2022 Jun;42(6):2827-2833

Short-term oral pre-exposure prophylaxis against HIV-1 modulates the transcriptome of foreskin tissue in young men in Africa.
Petkov S, Herrera C, Else L, Lebina L, Opoka D, Seiphetlo TB, Pillay AA, Mugaba S, Namubiru P, Odoch G, Ssemata AS, Serwanga J, Kaleebu P, Webb EL, Khoo S, Martinson N, Gray CM, Fox J, Chiodi F
Front Immunol 2022 ;13():1009978

Transcriptomic Profiling Reveals That HMGB1 Induces Macrophage Polarization Different from Classical M1.
Qu H, Heinbäck R, Salo H, Ewing E, Espinosa A, Aulin C, Erlandsson Harris H
Biomolecules 2022 Jun;12(6):

Plaque Evaluation by Ultrasound and Transcriptomics Reveals BCLAF1 as a Regulator of Smooth Muscle Cell Lipid Transdifferentiation in Atherosclerosis.
Rykaczewska U, Zhao Q, Saliba-Gustafsson P, Lengquist M, Kronqvist M, Bergman O, Huang Z, Lund K, Waden K, Pons Vila Z, Caidahl K, Skogsberg J, Vukojevic V, Lindeman JHN, Roy J, Hansson GK, Treuter E, Leeper NJ, Eriksson P, Ehrenborg E, Razuvaev A, Hedin U, Matic L
Arterioscler Thromb Vasc Biol 2022 May;42(5):659-676

CD45RA+CD62L- ILCs in human tissues represent a quiescent local reservoir for the generation of differentiated ILCs.
Kokkinou E, Pandey RV, Mazzurana L, Gutierrez-Perez I, Tibbitt CA, Weigel W, Soini T, Carrasco A, Rao A, Nagasawa M, Bal SM, Jangard M, Friberg D, Lindforss U, Nordenvall C, Ljunggren M, Haapaniemi S, Keita ÅV, Söderholm J, Hedin C, Spits H, Bryceson YT, Mjösberg J
Sci Immunol 2022 Apr;7(70):eabj8301

Human skin specific long noncoding RNA HOXC13-AS regulates epidermal differentiation by interfering with Golgi-ER retrograde transport.
Zhang L, Piipponen M, Liu Z, Li D, Bian X, Niu G, Geara J, Toma MA, Sommar P, Xu Landén N
Cell Death Differ 2023 May;30(5):1334-1348

An overlooked subset of Cx3cr1wt/wt microglia in the Cx3cr1CreER-Eyfp/wt mouse has a repopulation advantage over Cx3cr1CreER-Eyfp/wt microglia following microglial depletion.
Zhou K, Han J, Lund H, Boggavarapu NR, Lauschke VM, Goto S, Cheng H, Wang Y, Tachi A, Xie C, Zhu K, Sun Y, Osman AM, Liang D, Han W, Gemzell-Danielsson K, Betsholtz C, Zhang XM, Zhu C, Enge M, Joseph B, Harris RA, Blomgren K
J Neuroinflammation 2022 Jan;19(1):20

2021

Whole-Genome Metagenomic Analysis of the Gut Microbiome in HIV-1-Infected Individuals on Antiretroviral Therapy.
Bai X, Narayanan A, Nowak P, Ray S, Neogi U, Sönnerborg A
Front Microbiol 2021 ;12():667718

Regulation of Decay Accelerating Factor Primes Human Germinal Center B Cells for Phagocytosis.
Dernstedt A, Leidig J, Holm A, Kerkman PF, Mjösberg J, Ahlm C, Henriksson J, Hultdin M, Forsell MNE
Front Immunol 2020 ;11():599647

Spinal Cord Injury Induces Permanent Reprogramming of Microglia into a Disease-Associated State Which Contributes to Functional Recovery.
Hakim R, Zachariadis V, Sankavaram SR, Han J, Harris RA, Brundin L, Enge M, Svensson M
J Neurosci 2021 Oct;41(40):8441-8459

The corepressors GPS2 and SMRT control enhancer and silencer remodeling via eRNA transcription during inflammatory activation of macrophages.
Huang Z, Liang N, Goñi S, Damdimopoulos A, Wang C, Ballaire R, Jager J, Niskanen H, Han H, Jakobsson T, Bracken AP, Aouadi M, Venteclef N, Kaikkonen MU, Fan R, Treuter E
Mol Cell 2021 Mar;81(5):953-968.e9

A differential DNA methylome signature of pulmonary immune cells from individuals converting to latent tuberculosis infection.
Karlsson L, Das J, Nilsson M, Tyrén A, Pehrson I, Idh N, Sayyab S, Paues J, Ugarte-Gil C, Méndez-Aranda M, Lerm M
Sci Rep 2021 Sep;11(1):19418

Wnt ligands 3a and 5a regulate proliferation and migration in human fetal liver progenitor cells.
Liu Z, Kuna VK, Xu B, Sumitran-Holgersson S
Transl Gastroenterol Hepatol 2021 ;6():56

Polyvinyl Alcohol Carbazate as a Polymer-Based Antitumoral Agent.
Sellberg F, Fröbom R, Binder C, Berglund E, Berglund D
Front Oncol 2020 ;10():598394

High-resolution targeted bisulfite sequencing reveals blood cell type-specific DNA methylation patterns in IL13 and ORMDL3.
Söderhäll C, Reinius LE, Salmenperä P, Gentile M, Acevedo N, Konradsen JR, Nordlund B, Hedlin G, Scheynius A, Myllykangas S, Kere J
Clin Epigenetics 2021 May;13(1):106

2020

Dysregulation in Akt/mTOR/HIF-1 signaling identified by proteo-transcriptomics of SARS-CoV-2 infected cells.
Appelberg S, Gupta S, Svensson Akusjärvi S, Ambikan AT, Mikaeloff F, Saccon E, Végvári Á, Benfeitas R, Sperk M, Ståhlberg M, Krishnan S, Singh K, Penninger JM, Mirazimi A, Neogi U
Emerg Microbes Infect 2020 Dec;9(1):1748-1760

Loss of G protein pathway suppressor 2 in human adipocytes triggers lipid remodeling by upregulating ATP binding cassette subfamily G member 1.
Barilla S, Liang N, Mileti E, Ballaire R, Lhomme M, Ponnaiah M, Lemoine S, Soprani A, Gautier JF, Amri EZ, Le Goff W, Venteclef N, Treuter E
Mol Metab 2020 Dec;42():101066

Abo1 is required for the H3K9me2 to H3K9me3 transition in heterochromatin.
Dong W, Oya E, Zahedi Y, Prasad P, Svensson JP, Lennartsson A, Ekwall K, Durand-Dubief M
Sci Rep 2020 Apr;10(1):6055

Distinct developmental pathways from blood monocytes generate human lung macrophage diversity.
Evren E, Ringqvist E, Tripathi KP, Sleiers N, Rives IC, Alisjahbana A, Gao Y, Sarhan D, Halle T, Sorini C, Lepzien R, Marquardt N, Michaëlsson J, Smed-Sörensen A, Botling J, Karlsson MCI, Villablanca EJ, Willinger T
Immunity 2021 Feb;54(2):259-275.e7

Three months of bed rest induce a residual transcriptomic signature resilient to resistance exercise countermeasures.
Fernandez-Gonzalo R, Tesch PA, Lundberg TR, Alkner BA, Rullman E, Gustafsson T
FASEB J 2020 Jun;34(6):7958-7969

The DNA methyltransferase DNMT3A contributes to autophagy long-term memory.
González-Rodríguez P, Cheray M, Füllgrabe J, Salli M, Engskog-Vlachos P, Keane L, Cunha V, Lupa A, Li W, Ma Q, Dreij K, Rosenfeld MG, Joseph B
Autophagy 2021 May;17(5):1259-1277

DNA methylation in infants with low and high body fatness.
Henriksson P, Lentini A, Altmäe S, Brodin D, Müller P, Forsum E, Nestor CE, Löf M
BMC Genomics 2020 Nov;21(1):769

Hyperbaric oxygen preconditioning of ovarian tissue before cryopreservation modulate genes invilved in follicle activation and anti-apoptotic pathways
Kjellberg A, Diakaki C, Hao X, Anastacio A Rodriguez-Wallberg KA. https://doi.org/10.1016/j.fertnstert.2020.08.1041

Differentiation of ciliated human midbrain-derived LUHMES neurons.
Lauter G, Coschiera A, Yoshihara M, Sugiaman-Trapman D, Ezer S, Sethurathinam S, Katayama S, Kere J, Swoboda P
J Cell Sci 2020 Nov;133(21):

Radiation Triggers a Dynamic Sequence of Transient Microglial Alterations in Juvenile Brain.
Osman AM, Sun Y, Burns TC, He L, Kee N, Oliva-Vilarnau N, Alevyzaki A, Zhou K, Louhivuori L, Uhlén P, Hedlund E, Betsholtz C, Lauschke VM, Kele J, Blomgren K
Cell Rep 2020 Jun;31(9):107699

Glutamine Links Obesity to Inflammation in Human White Adipose Tissue.
Petrus P, Lecoutre S, Dollet L, Wiel C, Sulen A, Gao H, Tavira B, Laurencikiene J, Rooyackers O, Checa A, Douagi I, Wheelock CE, Arner P, McCarthy M, Bergo MO, Edgar L, Choudhury RP, Aouadi M, Krook A, Rydén M
Cell Metab 2020 Feb;31(2):375-390.e11

A regulatory role for CHD2 in myelopoiesis.
Shahin Varnoosfaderani F, Palau A, Dong W, Persson J, Durand-Dubief M, Svensson JP, Lennartsson A
Epigenetics 2020 ;15(6-7):702-714

2019

RITA downregulates Hedgehog-GLI in medulloblastoma and rhabdomyosarcoma via JNK-dependent but p53-independent mechanism.
Azatyan A, Gallo-Oller G, Diao Y, Selivanova G, Johnsen JI, Zaphiropoulos PG
Cancer Lett 2019 Feb;442():341-350

A preliminary transcriptome analysis suggests a transitory effect of vitamin D on mitochondrial function in obese young Finnish subjects.
Einarsdottir E, Pekkinen M, Krjutškov K, Katayama S, Kere J, Mäkitie O, Viljakainen H
Endocr Connect 2019 May;8(5):559-570

Non-parametric combination analysis of multiple data types enables detection of novel regulatory mechanisms in T cells of multiple sclerosis patients.
Fernandes SJ, Morikawa H, Ewing E, Ruhrmann S, Joshi RN, Lagani V, Karathanasis N, Khademi M, Planell N, Schmidt A, Tsamardinos I, Olsson T, Piehl F, Kockum I, Jagodic M, Tegnér J, Gomez-Cabrero D
Sci Rep 2019 Aug;9(1):11996

Type I IFN system activation in newborns exposed to Ro/SSA and La/SSB autoantibodies in utero.
Hedlund M, Thorlacius GE, Ivanchenko M, Ottosson V, Kyriakidis N, Lagnefeldt L, Tingström J, Sirsjö A, Bengtsson AA, Aronsson E, Gemzell-Danielsson K, Ronnblom L, Bergman G, Espinosa A, Sonesson SE, Eloranta ML, Wahren-Herlenius M
RMD Open 2020 Jan;6(1):

G protein pathway suppressor 2 (GPS2) links inflammation and cholesterol efflux by controlling lipopolysaccharide-induced ATP-binding cassette transporter A1 expression in macrophages.
Huang Z, Liang N, Damdimopoulos A, Fan R, Treuter E
FASEB J 2019 Feb;33(2):1631-1643

Human skin long noncoding RNA WAKMAR1 regulates wound healing by enhancing keratinocyte migration.
Li D, Kular L, Vij M, Herter EK, Li X, Wang A, Chu T, Toma MA, Zhang L, Liapi E, Mota A, Blomqvist L, Gallais Sérézal I, Rollman O, Wikstrom JD, Bienko M, Berglund D, Ståhle M, Sommar P, Jagodic M, Landén NX
Proc Natl Acad Sci U S A 2019 May;116(19):9443-9452

Hepatocyte-specific loss of GPS2 in mice reduces non-alcoholic steatohepatitis via activation of PPARα.
Liang N, Damdimopoulos A, Goñi S, Huang Z, Vedin LL, Jakobsson T, Giudici M, Ahmed O, Pedrelli M, Barilla S, Alzaid F, Mendoza A, Schröder T, Kuiper R, Parini P, Hollenberg A, Lefebvre P, Francque S, Van Gaal L, Staels B, Venteclef N, Treuter E, Fan R
Nat Commun 2019 Apr;10(1):1684

Leo1 is essential for the dynamic regulation of heterochromatin and gene expression during cellular quiescence.
Oya E, Durand-Dubief M, Cohen A, Maksimov V, Schurra C, Nakayama JI, Weisman R, Arcangioli B, Ekwall K
Epigenetics Chromatin 2019 Jul;12(1):45

Accumulation of Progerin Affects the Symmetry of Cell Division and Is Associated with Impaired Wnt Signaling and the Mislocalization of Nuclear Envelope Proteins.
Sola-Carvajal A, Revêchon G, Helgadottir HT, Whisenant D, Hagblom R, Döhla J, Katajisto P, Brodin D, Fagerström-Billai F, Viceconte N, Eriksson M
J Invest Dermatol 2019 Nov;139(11):2272-2280.e12

2018

Mixed-species RNAseq analysis of human lymphoma cells adhering to mouse stromal cells identifies a core gene set that is also differentially expressed in the lymph node microenvironment of mantle cell lymphoma and chronic lymphocytic leukemia patients.
Arvidsson G, Henriksson J, Sander B, Wright AP
Haematologica 2018 Apr;103(4):666-678

Study on genetic stability in human urothelial cells in vitro.
Chamorro CI, Zeiai S, Reinfeldt Engberg G, Brodin D, Lundin J, Nordenskjöld A, Fossum M
J Tissue Eng Regen Med 2018 Feb;12(2):e720-e726

An Expanded Role for the RFX Transcription Factor DAF-19, with Dual Functions in Ciliated and Nonciliated Neurons.
De Stasio EA, Mueller KP, Bauer RJ, Hurlburt AJ, Bice SA, Scholtz SL, Phirke P, Sugiaman-Trapman D, Stinson LA, Olson HB, Vogel SL, Ek-Vazquez Z, Esemen Y, Korzynski J, Wolfe K, Arbuckle BN, Zhang H, Lombard-Knapp G, Piasecki BP, Swoboda P
Genetics 2018 Mar;208(3):1083-1097

The chromatin-remodeling factor CHD4 is required for maintenance of childhood acute myeloid leukemia.
Heshmati Y, Türköz G, Harisankar A, Kharazi S, Boström J, Dolatabadi EK, Krstic A, Chang D, Månsson R, Altun M, Qian H, Walfridsson J
Haematologica 2018 Jul;103(7):1169-1181

Whole genome microarray expression analysis in blood identifies pathways linked to signs and symptoms of a patient with hypercalprotectinaemia and hyperzincaemia.
Isaksson HS, Farkas SA, Müller P, Gustafsson D, Nilsson TK
Clin Exp Immunol 2018 Feb;191(2):240-251

DNA methylation as a mediator of HLA-DRB1*15:01 and a protective variant in multiple sclerosis.
Kular L, Liu Y, Ruhrmann S, Zheleznyakova G, Marabita F, Gomez-Cabrero D, James T, Ewing E, Lindén M, Górnikiewicz B, Aeinehband S, Stridh P, Link J, Andlauer TFM, Gasperi C, Wiendl H, Zipp F, Gold R, Tackenberg B, Weber F, Hemmer B, Strauch K, Heilmann-Heimbach S, Rawal R, Schminke U, Schmidt CO, Kacprowski T, Franke A, Laudes M, Dilthey AT, Celius EG, Søndergaard HB, Tegnér J, Harbo HF, Oturai AB, Olafsson S, Eggertsson HP, Halldorsson BV, Hjaltason H, Olafsson E, Jonsdottir I, Stefansson K, Olsson T, Piehl F, Ekström TJ, Kockum I, Feinberg AP, Jagodic M
Nat Commun 2018 Jun;9(1):2397

Competitive repopulation of an empty microglial niche yields functionally distinct subsets of microglia-like cells.
Lund H, Pieber M, Parsa R, Han J, Grommisch D, Ewing E, Kular L, Needhamsen M, Espinosa A, Nilsson E, Överby AK, Butovsky O, Jagodic M, Zhang XM, Harris RA
Nat Commun 2018 Nov;9(1):4845

Testis transcriptome alterations in zebrafish (Danio rerio) with reduced fertility due to developmental exposure to 17α-ethinyl estradiol.
Porseryd T, Reyhanian Caspillo N, Volkova K, Elabbas L, Källman T, Dinnétz P, Olsson PE, Porsch-Hällström I
Gen Comp Endocrinol 2018 Jun;262():44-58

TAC-seq: targeted DNA and RNA sequencing for precise biomarker molecule counting.
Teder H, Koel M, Paluoja P, Jatsenko T, Rekker K, Laisk-Podar T, Kukuškina V, Velthut-Meikas A, Fjodorova O, Peters M, Kere J, Salumets A, Palta P, Krjutškov K
NPJ Genom Med 2018 ;3():34

Human pluripotent reprogramming with CRISPR activators.
Weltner J, Balboa D, Katayama S, Bespalov M, Krjutškov K, Jouhilahti EM, Trokovic R, Kere J, Otonkoski T
Nat Commun 2018 Jul;9(1):2643

2017

Single cell transcriptomics suggest that human adipocyte progenitor cells constitute a homogeneous cell population.
Acosta JR, Joost S, Karlsson K, Ehrlund A, Li X, Aouadi M, Kasper M, Arner P, Rydén M, Laurencikiene J
Stem Cell Res Ther 2017 Nov;8(1):250

Grandpaternal-induced transgenerational dietary reprogramming of the unfolded protein response in skeletal muscle.
Alm PS, de Castro Barbosa T, Barrès R, Krook A, Zierath JR
Mol Metab 2017 Jul;6(7):621-630

Host knockout of E-prostanoid 2 receptors reduces tumor growth and causes major alterations of gene expression in prostaglandin E2-producing tumors.
Asting AG, Iresjö BM, Nilsberth C, Smedh U, Lundholm K
Oncol Lett 2017 Jan;13(1):476-482

Hepatitis C Virus-Specific T Cell Receptor mRNA-Engineered Human T Cells: Impact of Antigen Specificity on Functional Properties.
Balasiddaiah A, Davanian H, Aleman S, Pasetto A, Frelin L, Sällberg M, Lohmann V, Koh S, Bertoletti A, Chen M
J Virol 2017 May;91(9):

DNA alterations in Cd133+ and Cd133- tumour cells enriched from intra-operative human colon tumour biopsies.
Cervantes-Madrid D, Wettergren Y, Falk P, Lundholm K, Asting AG
BMC Cancer 2017 Mar;17(1):219

Interplay of Energetics and ER Stress Exacerbates Alzheimer's Amyloid-β (Aβ) Toxicity in Yeast.
Chen X, Bisschops MMM, Agarwal NR, Ji B, Shanmugavel KP, Petranovic D
Front Mol Neurosci 2017 ;10():232

Ameloblastoma RNA profiling uncovers a distinct non-coding RNA signature.
Davanian H, Balasiddaiah A, Heymann R, Sundström M, Redenström P, Silfverberg M, Brodin D, Sällberg M, Lindskog S, Kruger Weiner C, Chen M
Oncotarget 2017 Jan;8(3):4530-4542

The cell-type specific transcriptome in human adipose tissue and influence of obesity on adipocyte progenitors.
Ehrlund A, Acosta JR, Björk C, Hedén P, Douagi I, Arner P, Laurencikiene J
Sci Data 2017 Oct;4():170164

Human Herpesvirus 6B Induces Hypomethylation on Chromosome 17p13.3, Correlating with Increased Gene Expression and Virus Integration.
Engdahl E, Dunn N, Niehusmann P, Wideman S, Wipfler P, Becker AJ, Ekström TJ, Almgren M, Fogdell-Hahn A
J Virol 2017 Jun;91(11):

MicroRNA-132 with Therapeutic Potential in Chronic Wounds.
Li X, Li D, Wang A, Chu T, Lohcharoenkal W, Zheng X, Grünler J, Narayanan S, Eliasson S, Herter EK, Wang Y, Ma Y, Ehrström M, Eidsmo L, Kasper M, Pivarcsi A, Sonkoly E, Catrina SB, Ståhle M, Xu Landén N
J Invest Dermatol 2017 Dec;137(12):2630-2638

Smoking induces DNA methylation changes in Multiple Sclerosis patients with exposure-response relationship.
Marabita F, Almgren M, Sjöholm LK, Kular L, Liu Y, James T, Kiss NB, Feinberg AP, Olsson T, Kockum I, Alfredsson L, Ekström TJ, Jagodic M
Sci Rep 2017 Nov;7(1):14589

Hypomethylation of HOXA4 promoter is common in Silver-Russell syndrome and growth restriction and associates with stature in healthy children.
Muurinen M, Hannula-Jouppi K, Reinius LE, Söderhäll C, Merid SK, Bergström A, Melén E, Pershagen G, Lipsanen-Nyman M, Greco D, Kere J
Sci Rep 2017 Nov;7(1):15693

Usability of human Infinium MethylationEPIC BeadChip for mouse DNA methylation studies.
Needhamsen M, Ewing E, Lund H, Gomez-Cabrero D, Harris RA, Kular L, Jagodic M
BMC Bioinformatics 2017 Nov;18(1):486

Persistent Effects of Developmental Exposure to 17α-Ethinylestradiol on the Zebrafish (Danio rerio) Brain Transcriptome and Behavior.
Porseryd T, Volkova K, Reyhanian Caspillo N, Källman T, Dinnetz P, Porsh Hällström I
Front Behav Neurosci 2017 ;11():69

IL-7δ5 protein is expressed in human tissues and induces expression of the oxidized low density lipoprotein receptor 1 (OLR1) in CD14+ monocytes.
Rane L, Rahman S, Magalhaes I, Ambati A, Andersson J, Zumla A, Brighenti S, Maeurer MJ
Int J Infect Dis 2017 Jun;59():29-36

Transcriptional response to 131I exposure of rat thyroid gland.
Rudqvist N, Spetz J, Schüler E, Parris TZ, Langen B, Helou K, Forssell-Aronsson E
PLoS One 2017 ;12(2):e0171797

Hypermethylation of MIR21 in CD4+ T cells from patients with relapsing-remitting multiple sclerosis associates with lower miRNA-21 levels and concomitant up-regulation of its target genes.
Ruhrmann S, Ewing E, Piket E, Kular L, Cetrulo Lorenzi JC, Fernandes SJ, Morikawa H, Aeinehband S, Sayols-Baixeras S, Aslibekyan S, Absher DM, Arnett DK, Tegner J, Gomez-Cabrero D, Piehl F, Jagodic M
Mult Scler 2018 Sep;24(10):1288-1300

Comprehensive mapping of the effects of azacitidine on DNA methylation, repressive/permissive histone marks and gene expression in primary cells from patients with MDS and MDS-related disease.
Tobiasson M, Abdulkadir H, Lennartsson A, Katayama S, Marabita F, De Paepe A, Karimi M, Krjutskov K, Einarsdottir E, Grövdal M, Jansson M, Ben Azenkoud A, Corddedu L, Lehmann S, Ekwall K, Kere J, Hellström-Lindberg E, Ungerstedt J
Oncotarget 2017 Apr;8(17):28812-28825

Functional genomics analysis of vitamin D effects on CD4+ T cells in vivo in experimental autoimmune encephalomyelitis ‬.
Zeitelhofer M, Adzemovic MZ, Gomez-Cabrero D, Bergman P, Hochmeister S, N'diaye M, Paulson A, Ruhrmann S, Almgren M, Tegnér JN, Ekström TJ, Guerreiro-Cacais AO, Jagodic M
Proc Natl Acad Sci U S A 2017 Feb;114(9):E1678-E1687

2016

Tissue and Serum miRNA Profile in Locally Advanced Breast Cancer (LABC) in Response to Neo-Adjuvant Chemotherapy (NAC) Treatment.
Al-Khanbashi M, Caramuta S, Alajmi AM, Al-Haddabi I, Al-Riyami M, Lui WO, Al-Moundhri MS
PLoS One 2016 ;11(4):e0152032

A role for PDGF-C/PDGFRα signaling in the formation of the meningeal basement membranes surrounding the cerebral cortex.
Andrae J, Gouveia L, Gallini R, He L, Fredriksson L, Nilsson I, Johansson BR, Eriksson U, Betsholtz C
Biol Open 2016 Apr;5(4):461-74

Alterations in Tumor DNA Are Related to Short Postoperative Survival in Patients Resected for Pancreatic Carcinoma Aimed at Cure.
Asting AG, Ljungman D, Carén H, Dambrauskas Z, Iresjö BM, Hyltander A, Naredi P, Lundholm K
Pancreas 2016 Jul;45(6):900-7

Cellular High-Energy Cavitation Trauma - Description of a Novel In Vitro Trauma Model in Three Different Cell Types.
Cao Y, Risling M, Malm E, Sondén A, Bolling MF, Sköld MK
Front Neurol 2016 ;7():10

Numerous Genes in Loci Associated With Body Fat Distribution Are Linked to Adipose Function.
Dahlman I, Rydén M, Brodin D, Grallert H, Strawbridge RJ, Arner P
Diabetes 2016 Feb;65(2):433-7

Regulation of myeloid cells by activated T cells determines the efficacy of PD-1 blockade.
Eissler N, Mao Y, Brodin D, Reuterswärd P, Andersson Svahn H, Johnsen JI, Kiessling R, Kogner P
Oncoimmunology 2016 ;5(12):e1232222

Stromal Hedgehog signalling is downregulated in colon cancer and its restoration restrains tumour growth.
Gerling M, Büller NV, Kirn LM, Joost S, Frings O, Englert B, Bergström Å, Kuiper RV, Blaas L, Wielenga MC, Almer S, Kühl AA, Fredlund E, van den Brink GR, Toftgård R
Nat Commun 2016 Aug;7():12321

Preoperative overnight parenteral nutrition (TPN) improves skeletal muscle protein metabolism indicated by microarray algorithm analyses in a randomized trial.
Iresjö BM, Engström C, Lundholm K
Physiol Rep 2016 Jun;4(11):

Single-cell transcriptome analysis of endometrial tissue.
Krjutškov K, Katayama S, Saare M, Vera-Rodriguez M, Lubenets D, Samuel K, Laisk-Podar T, Teder H, Einarsdottir E, Salumets A, Kere J
Hum Reprod 2016 Apr;31(4):844-53

Gene-Expression Profiling Suggests Impaired Signaling via the Interferon Pathway in Cstb-/- Microglia.
Körber I, Katayama S, Einarsdottir E, Krjutškov K, Hakala P, Kere J, Lehesjoki AE, Joensuu T
PLoS One 2016 ;11(6):e0158195

Aerobic exercise augments muscle transcriptome profile of resistance exercise.
Lundberg TR, Fernandez-Gonzalo R, Tesch PA, Rullman E, Gustafsson T
Am J Physiol Regul Integr Comp Physiol 2016 Jun;310(11):R1279-87

Independent control of natural killer cell responsiveness and homeostasis at steady-state by CD11c+ dendritic cells.
Luu TT, Ganesan S, Wagner AK, Sarhan D, Meinke S, Garbi N, Hämmerling G, Alici E, Kärre K, Chambers BJ, Höglund P, Kadri N
Sci Rep 2016 Dec;6():37996

Wnt/β-Catenin Stimulation and Laminins Support Cardiovascular Cell Progenitor Expansion from Human Fetal Cardiac Mesenchymal Stromal Cells.
Månsson-Broberg A, Rodin S, Bulatovic I, Ibarra C, Löfling M, Genead R, Wärdell E, Felldin U, Granath C, Alici E, Le Blanc K, Smith CIE, Salašová A, Westgren M, Sundström E, Uhlén P, Arenas E, Sylvén C, Tryggvason K, Corbascio M, Simonson OE, Österholm C, Grinnemo KH
Stem Cell Reports 2016 Apr;6(4):607-617

Regulating retrotransposon activity through the use of alternative transcription start sites.
Persson J, Steglich B, Smialowska A, Boyd M, Bornholdt J, Andersson R, Schurra C, Arcangioli B, Sandelin A, Nielsen O, Ekwall K
EMBO Rep 2016 May;17(5):753-68

The transcriptional coregulator MAML1 affects DNA methylation and gene expression patterns in human embryonic kidney cells.
Putnik M, Brodin D, Wojdacz TK, Fagerström-Billai F, Dahlman-Wright K, Wallberg AE
Mol Biol Rep 2016 Mar;43(3):141-50

mRNA and microRNA transcriptomics analyses in a murine model of dystrophin loss and therapeutic restoration.
Roberts TC, Blomberg KE, Smith CI, El Andaloussi S, Wood MJ
Genom Data 2016 Mar;7():88-9

Cells release subpopulations of exosomes with distinct molecular and biological properties.
Willms E, Johansson HJ, Mäger I, Lee Y, Blomberg KE, Sadik M, Alaarg A, Smith CI, Lehtiö J, El Andaloussi S, Wood MJ, Vader P
Sci Rep 2016 Mar;6():22519

2015

Expression of progerin in aging mouse brains reveals structural nuclear abnormalities without detectible significant alterations in gene expression, hippocampal stem cells or behavior.
Baek JH, Schmidt E, Viceconte N, Strandgren C, Pernold K, Richard TJ, Van Leeuwen FW, Dantuma NP, Damberg P, Hultenby K, Ulfhake B, Mugnaini E, Rozell B, Eriksson M
Hum Mol Genet 2015 Mar;24(5):1305-21

Induction of USP17 by combining BET and HDAC inhibitors in breast cancer cells.
Borbely G, Haldosen LA, Dahlman-Wright K, Zhao C
Oncotarget 2015 Oct;6(32):33623-35

A study on proliferation and gene expression in normal human urothelial cells in culture.
Chamorro CI, Zeiai S, Engberg GR, Brodin D, Nordenskjöld A, Fossum M
Tissue Eng Part A 2015 Feb;21(3-4):510-7

The fat cell epigenetic signature in post-obese women is characterized by global hypomethylation and differential DNA methylation of adipogenesis genes.
Dahlman I, Sinha I, Gao H, Brodin D, Thorell A, Rydén M, Andersson DP, Henriksson J, Perfilyev A, Ling C, Dahlman-Wright K, Arner P
Int J Obes (Lond) 2015 Jun;39(6):910-9

Cytostatic Effect of Repeated Exposure to Simvastatin: A Mechanism for Chronic Myotoxicity Revealed by the Use of Mesodermal Progenitors Derived from Human Pluripotent Stem Cells.
Peric D, Barragan I, Giraud-Triboult K, Egesipe AL, Meyniel-Schicklin L, Cousin C, Lotteau V, Petit V, Touhami J, Battini JL, Sitbon M, Pinset C, Ingelman-Sundberg M, Laustriat D, Peschanski M
Stem Cells 2015 Oct;33(10):2936-48

mRNA and microRNA transcriptomics analyses in a murine model of dystrophin loss and therapeutic restoration.
Roberts TC, Blomberg KE, Smith CI, El Andaloussi S, Wood MJ
Genom Data 2016 Mar;7():88-9

Temporal analysis of reciprocal miRNA-mRNA expression patterns predicts regulatory networks during differentiation in human skeletal muscle cells.
Sjögren RJ, Egan B, Katayama M, Zierath JR, Krook A
Physiol Genomics 2015 Mar;47(3):45-57

2014

Risk of childhood asthma is associated with CpG-site polymorphisms, regional DNA methylation and mRNA levels at the GSDMB/ORMDL3 locus.
Acevedo N, Reinius LE, Greco D, Gref A, Orsmark-Pietras C, Persson H, Pershagen G, Hedlin G, Melén E, Scheynius A, Kere J, Söderhäll C
Hum Mol Genet 2015 Feb;24(3):875-90

Superselective intra-arterial umbilical cord blood administration to BM in experimental animals.
Arnberg F, Lundberg J, Kenne E, Jaff N, Müller P, Nava S, Kaipe H, Ringdén O, Holmin S
Bone Marrow Transplant 2014 Dec;49(12):1486-91

The human carotid body releases acetylcholine, ATP and cytokines during hypoxia.
Kåhlin J, Mkrtchian S, Ebberyd A, Hammarstedt-Nordenvall L, Nordlander B, Yoshitake T, Kehr J, Prabhakar N, Poellinger L, Fagerlund MJ, Eriksson LI
Exp Physiol 2014 Aug;99(8):1089-98

Medium from γ-irradiated Escherichia coli bacteria stimulates a unique immune response in Drosophila cells.
Lindberg BG, Oldenvi S, Steiner H
Dev Comp Immunol 2014 Oct;46(2):392-400

MiR-146a negatively regulates TLR2-induced inflammatory responses in keratinocytes.
Meisgen F, Xu Landén N, Wang A, Réthi B, Bouez C, Zuccolo M, Gueniche A, Ståhle M, Sonkoly E, Breton L, Pivarcsi A
J Invest Dermatol 2014 Jul;134(7):1931-1940

High-throughput transcription profiling identifies putative epigenetic regulators of hematopoiesis.
Prasad P, Rönnerblad M, Arner E, Itoh M, Kawaji H, Lassmann T, Daub CO, Forrest AR, Lennartsson A, Ekwall K, 
Blood 2014 Apr;123(17):e46-57

Analysis of the DNA methylome and transcriptome in granulopoiesis reveals timed changes and dynamic enhancer methylation.
Rönnerblad M, Andersson R, Olofsson T, Douagi I, Karimi M, Lehmann S, Hoof I, de Hoon M, Itoh M, Nagao-Sato S, Kawaji H, Lassmann T, Carninci P, Hayashizaki Y, Forrest AR, Sandelin A, Ekwall K, Arner E, Lennartsson A, 
Blood 2014 Apr;123(17):e79-89

Centromeric histone H2B monoubiquitination promotes noncoding transcription and chromatin integrity.
Sadeghi L, Siggens L, Svensson JP, Ekwall K
Nat Struct Mol Biol 2014 Mar;21(3):236-43

The DEK oncoprotein binds to highly and ubiquitously expressed genes with a dual role in their transcriptional regulation.
Sandén C, Järvstråt L, Lennartsson A, Brattås PL, Nilsson B, Gullberg U
Mol Cancer 2014 Sep;13():215

Fish oil and krill oil supplementations differentially regulate lipid catabolic and synthetic pathways in mice.
Tillander V, Bjørndal B, Burri L, Bohov P, Skorve J, Berge RK, Alexson SE
Nutr Metab (Lond) 2014 ;11():20

Genome-wide profiling of AP-1-regulated transcription provides insights into the invasiveness of triple-negative breast cancer.
Zhao C, Qiao Y, Jonsson P, Wang J, Xu L, Rouhi P, Sinha I, Cao Y, Williams C, Dahlman-Wright K
Cancer Res 2014 Jul;74(14):3983-94

The atypical ubiquitin ligase RNF31 stabilizes estrogen receptor α and modulates estrogen-stimulated breast cancer cell proliferation.
Zhu J, Zhao C, Razavirad A, Zhuang T, Jonsson P, Liang N, Williams C, Lin CY, Qiao Y, Zendehdel K, Strömblad S, Treuter E, Dahlman-Wright K
Oncogene 2014 Aug;33(34):4340-51

2013

Imatinib ameliorates neuroinflammation in a rat model of multiple sclerosis by enhancing blood-brain barrier integrity and by modulating the peripheral immune response.
Adzemovic MV, Zeitelhofer M, Eriksson U, Olsson T, Nilsson I
PLoS One 2013 ;8(2):e56586

Active transcriptomic and proteomic reprogramming in the C. elegans nucleotide excision repair mutant xpa-1.
Arczewska KD, Tomazella GG, Lindvall JM, Kassahun H, Maglioni S, Torgovnick A, Henriksson J, Matilainen O, Marquis BJ, Nelson BC, Jaruga P, Babaie E, Holmberg CI, Bürglin TR, Ventura N, Thiede B, Nilsen H
Nucleic Acids Res 2013 May;41(10):5368-81

The Oct1 homolog Nubbin is a repressor of NF-κB-dependent immune gene expression that increases the tolerance to gut microbiota.
Dantoft W, Davis MM, Lindvall JM, Tang X, Uvell H, Junell A, Beskow A, Engström Y
BMC Biol 2013 Sep;11():99

DNA damage leads to progressive replicative decline but extends the life span of long-lived mutant animals.
Lans H, Lindvall JM, Thijssen K, Karambelas AE, Cupac D, Fensgård O, Jansen G, Hoeijmakers JH, Nilsen H, Vermeulen W
Cell Death Differ 2013 Dec;20(12):1709-18

Global microRNA profiling of well-differentiated small intestinal neuroendocrine tumors.
Li SC, Essaghir A, Martijn C, Lloyd RV, Demoulin JB, Oberg K, Giandomenico V
Mod Pathol 2013 May;26(5):685-96

An evaluation of analysis pipelines for DNA methylation profiling using the Illumina HumanMethylation450 BeadChip platform.
Marabita F, Almgren M, Lindholm ME, Ruhrmann S, Fagerström-Billai F, Jagodic M, Sundberg CJ, Ekström TJ, Teschendorff AE, Tegnér J, Gomez-Cabrero D
Epigenetics 2013 Mar;8(3):333-46

DNA topoisomerase III localizes to centromeres and affects centromeric CENP-A levels in fission yeast.
Norman-Axelsson U, Durand-Dubief M, Prasad P, Ekwall K
PLoS Genet 2013 ;9(3):e1003371

Gene expression deregulation in postnatal skeletal muscle of TK2 deficient mice reveals a lower pool of proliferating myogenic progenitor cells.
Paredes JA, Zhou X, Höglund S, Karlsson A
PLoS One 2013 ;8(1):e53698

DNA methylation in the Neuropeptide S Receptor 1 (NPSR1) promoter in relation to asthma and environmental factors.
Reinius LE, Gref A, Sääf A, Acevedo N, Joerink M, Kupczyk M, D'Amato M, Bergström A, Melén E, Scheynius A, Dahlén SE, , Pershagen G, Söderhäll C, Kere J
PLoS One 2013 ;8(1):e53877

Early-phase GVHD gene expression profile in target versus non-target tissues: kidney, a possible target?
Sadeghi B, Al-Chaqmaqchi H, Al-Hashmi S, Brodin D, Hassan Z, Abedi-Valugerdi M, Moshfegh A, Hassan M
Bone Marrow Transplant 2013 Feb;48(2):284-93

Chronic airway-induced allergy in mice modifies gene expression in the brain toward insulin resistance and inflammatory responses.
Sarlus H, Wang X, Cedazo-Minguez A, Schultzberg M, Oprica M
J Neuroinflammation 2013 Aug;10():99

Combining genetic mapping with genome-wide expression in experimental autoimmune encephalomyelitis highlights a gene network enriched for T cell functions and candidate genes regulating autoimmunity.
Thessen Hedreul M, Möller S, Stridh P, Gupta Y, Gillett A, Daniel Beyeen A, Öckinger J, Flytzani S, Diez M, Olsson T, Jagodic M
Hum Mol Genet 2013 Dec;22(24):4952-66

2012

Stabilizing mutation of CTNNB1/beta-catenin and protein accumulation analyzed in a large series of parathyroid tumors of Swedish patients.
Björklund P, Lindberg D, Akerström G, Westin G
Mol Cancer 2008 Jun;7():53

Prediction of ischemic events on the basis of transcriptomic and genomic profiling in patients undergoing carotid endarterectomy.
Folkersen L, Persson J, Ekstrand J, Agardh HE, Hansson GK, Gabrielsen A, Hedin U, Paulsson-Berne G
Mol Med 2012 May;18(1):669-75

Differential evolutionary wiring of the tyrosine kinase Btk.
Nawaz HM, Kylsten P, Hamada N, Yamamoto D, Smith CI, Lindvall JM
PLoS One 2012 ;7(5):e35640

Transcriptome analysis reveals upregulation of bitter taste receptors in severe asthmatics.
Orsmark-Pietras C, James A, Konradsen JR, Nordlund B, Söderhäll C, Pulkkinen V, Pedroletti C, Daham K, Kupczyk M, Dahlén B, Kere J, Dahlén SE, Hedlin G, Melén E
Eur Respir J 2013 Jul;42(1):65-78

Differential DNA methylation in purified human blood cells: implications for cell lineage and studies on disease susceptibility.
Reinius LE, Acevedo N, Joerink M, Pershagen G, Dahlén SE, Greco D, Söderhäll C, Scheynius A, Kere J
PLoS One 2012 ;7(7):e41361

Expression analysis in multiple muscle groups and serum reveals complexity in the microRNA transcriptome of the mdx mouse with implications for therapy.
Roberts TC, Blomberg KE, McClorey G, El Andaloussi S, Godfrey C, Betts C, Coursindel T, Gait MJ, Smith CI, Wood MJ
Mol Ther Nucleic Acids 2012 Aug;1(8):e39

Toll-like receptor 7 protects from atherosclerosis by constraining "inflammatory" macrophage activation.
Salagianni M, Galani IE, Lundberg AM, Davos CH, Varela A, Gavriil A, Lyytikäinen LP, Lehtimäki T, Sigala F, Folkersen L, Gorgoulis V, Lenglet S, Montecucco F, Mach F, Hedin U, Hansson GK, Monaco C, Andreakos E
Circulation 2012 Aug;126(8):952-62

Effects of redox modulation by inhibition of thioredoxin reductase on radiosensitivity and gene expression.
Selenius M, Hedman M, Brodin D, Gandin V, Rigobello MP, Flygare J, Marzano C, Bindoli A, Brodin O, Björnstedt M, Fernandes AP
J Cell Mol Med 2012 Jul;16(7):1593-605

Genome-wide and locus specific alterations in CDC73/HRPT2-mutated parathyroid tumors.
Sulaiman L, Haglund F, Hashemi J, Obara T, Nordenström J, Larsson C, Juhlin CC
PLoS One 2012 ;7(9):e46325

MicroRNA-125b down-regulates matrix metallopeptidase 13 and inhibits cutaneous squamous cell carcinoma cell proliferation, migration, and invasion.
Xu N, Zhang L, Meisgen F, Harada M, Heilborn J, Homey B, Grandér D, Ståhle M, Sonkoly E, Pivarcsi A
J Biol Chem 2012 Aug;287(35):29899-908

2011

Altered mRNA expression due to acute mesenteric ischaemia in a porcine model.
Block T, Isaksson HS, Acosta S, Björck M, Brodin D, Nilsson TK
Eur J Vasc Endovasc Surg 2011 Feb;41(2):281-7

Prognostic DNA methylation patterns in cytogenetically normal acute myeloid leukemia are predefined by stem cell chromatin marks.
Deneberg S, Guardiola P, Lennartsson A, Qu Y, Gaidzik V, Blanchet O, Karimi M, Bengtzén S, Nahi H, Uggla B, Tidefelt U, Höglund M, Paul C, Ekwall K, Döhner K, Lehmann S
Blood 2011 Nov;118(20):5573-82

Genetic association and gene expression analysis identify FGFR1 as a new susceptibility gene for human obesity.
Jiao H, Arner P, Dickson SL, Vidal H, Mejhert N, Henegar C, Taube M, Hansson C, Hinney A, Galan P, Simon C, Silveira A, Benrick A, Jansson JO, Bouloumié A, Langin D, Laville M, Debard C, Axelsson T, Rydén M, Kere J, Dahlman-Wright K, Hamsten A, Clement K, Dahlman I
J Clin Endocrinol Metab 2011 Jun;96(6):E962-6

Genome wide association study identifies KCNMA1 contributing to human obesity.
Jiao H, Arner P, Hoffstedt J, Brodin D, Dubern B, Czernichow S, van't Hooft F, Axelsson T, Pedersen O, Hansen T, Sørensen TI, Hebebrand J, Kere J, Dahlman-Wright K, Hamsten A, Clement K, Dahlman I
BMC Med Genomics 2011 Jun;4():51

Reactive astrocytes and Wnt/β-catenin signaling link nigrostriatal injury to repair in 1-methyl-4-phenyl-1,2,3,6-tetrahydropyridine model of Parkinson's disease.
L'Episcopo F, Tirolo C, Testa N, Caniglia S, Morale MC, Cossetti C, D'Adamo P, Zardini E, Andreoni L, Ihekwaba AE, Serra PA, Franciotta D, Martino G, Pluchino S, Marchetti B
Neurobiol Dis 2011 Feb;41(2):508-27

Early transcriptional regulation by C-peptide in freshly isolated rat proximal tubular cells.
Lindahl E, Nordquist L, Müller P, El Agha E, Friederich M, Dahlman-Wright K, Palm F, Jörnvall H
Diabetes Metab Res Rev 2011 Oct;27(7):697-704

Transcriptional profiling of C. elegans DAF-19 uncovers a ciliary base-associated protein and a CDK/CCRK/LF2p-related kinase required for intraflagellar transport.
Phirke P, Efimenko E, Mohan S, Burghoorn J, Crona F, Bakhoum MW, Trieb M, Schuske K, Jorgensen EM, Piasecki BP, Leroux MR, Swoboda P
Dev Biol 2011 Sep;357(1):235-47

SWI/SNF regulates the alternative processing of a specific subset of pre-mRNAs in Drosophila melanogaster.
Waldholm J, Wang Z, Brodin D, Tyagi A, Yu S, Theopold U, Farrants AK, Visa N
BMC Mol Biol 2011 Nov;12():46

Histone modifications influence mediator interactions with chromatin.
Zhu X, Zhang Y, Bjornsdottir G, Liu Z, Quan A, Costanzo M, Dávila López M, Westholm JO, Ronne H, Boone C, Gustafsson CM, Myers LC
Nucleic Acids Res 2011 Oct;39(19):8342-54

Specific syndecan-1 domains regulate mesenchymal tumor cell adhesion, motility and migration.
Zong F, Fthenou E, Mundt F, Szatmári T, Kovalszky I, Szilák L, Brodin D, Tzanakakis G, Hjerpe A, Dobra K
PLoS One 2011 ;6(6):e14816

2010

Genetic evidence of multiple loci in dystocia--difficult labour.
Algovik M, Kivinen K, Peterson H, Westgren M, Kere J
BMC Med Genet 2010 Jun;11():105

Connective tissue growth factor is expressed in malignant cells of Hodgkin lymphoma but not in other mature B-cell lymphomas.
Birgersdotter A, Baumforth KR, Wei W, Murray PG, Sjöberg J, Björkholm M, Porwit A, Ernberg I
Am J Clin Pathol 2010 Feb;133(2):271-80

MGAT5 alters the severity of multiple sclerosis.
Brynedal B, Wojcik J, Esposito F, Debailleul V, Yaouanq J, Martinelli-Boneschi F, Edan G, Comi G, Hillert J, Abderrahim H
J Neuroimmunol 2010 Mar;220(1-2):120-4

Gene expression analysis in hypoplastic lungs in the nitrofen model of congenital diaphragmatic hernia.
Burgos CM, Uggla AR, Fagerström-Billai F, Eklöf AC, Frenckner B, Nord M
J Pediatr Surg 2010 Jul;45(7):1445-54

Analysis of oestrogen regulation of alpha-, beta- and gamma-secretase gene and protein expression in cultured human neuronal and glial cells.
Nord LC, Sundqvist J, Andersson E, Fried G
Neurodegener Dis 2010 ;7(6):349-64

Adipose tissue pathways involved in weight loss of cancer cachexia.
Dahlman I, Mejhert N, Linder K, Agustsson T, Mutch DM, Kulyte A, Isaksson B, Permert J, Petrovic N, Nedergaard J, Sjölin E, Brodin D, Clement K, Dahlman-Wright K, Rydén M, Arner P
Br J Cancer 2010 May;102(10):1541-8

Gene-specific and global methylation patterns predict outcome in patients with acute myeloid leukemia.
Deneberg S, Grövdal M, Karimi M, Jansson M, Nahi H, Corbacioglu A, Gaidzik V, Döhner K, Paul C, Ekström TJ, Hellström-Lindberg E, Lehmann S
Leukemia 2010 May;24(5):932-41

Topoisomerase I regulates open chromatin and controls gene expression in vivo.
Durand-Dubief M, Persson J, Norman U, Hartsuiker E, Ekwall K
EMBO J 2010 Jul;29(13):2126-34

Tissue factor pathway inhibitor-2 is induced by fluid shear stress in vascular smooth muscle cells and affects cell proliferation and survival.
Ekstrand J, Razuvaev A, Folkersen L, Roy J, Hedin U
J Vasc Surg 2010 Jul;52(1):167-75

Sustained inflammation due to nuclear factor-kappa B activation in irradiated human arteries.
Halle M, Gabrielsen A, Paulsson-Berne G, Gahm C, Agardh HE, Farnebo F, Tornvall P
J Am Coll Cardiol 2010 Mar;55(12):1227-1236

A chromatin-remodeling protein is a component of fission yeast mediator.
Khorosjutina O, Wanrooij PH, Walfridsson J, Szilagyi Z, Zhu X, Baraznenok V, Ekwall K, Gustafsson CM
J Biol Chem 2010 Sep;285(39):29729-37

The impact of RNA standardization and heterogeneous gene expression on the results of cDNA array of human breast carcinoma.
Khoshnoud R, He Q, Sylván M, Khoshnoud A, Ivarsson M, Fornander T, Bergh J, Frisell J, Rutqvist LE, Skog S
Int J Mol Med 2010 May;25(5):735-41

Schizosaccharomyces pombe genome-wide nucleosome mapping reveals positioning mechanisms distinct from those of Saccharomyces cerevisiae.
Lantermann AB, Straub T, Strålfors A, Yuan GC, Ekwall K, Korber P
Nat Struct Mol Biol 2010 Feb;17(2):251-7

Mapping of the fibroblast growth factors in human white adipose tissue.
Mejhert N, Galitzky J, Pettersson AT, Bambace C, Blomqvist L, Bouloumié A, Frayn KN, Dahlman I, Arner P, Rydén M
J Clin Endocrinol Metab 2010 May;95(5):2451-7

Molecular make-up of the glomerular filtration barrier.
Patrakka J, Tryggvason K
Biochem Biophys Res Commun 2010 May;396(1):164-9

Chd1 remodelers maintain open chromatin and regulate the epigenetics of differentiation.
Persson J, Ekwall K
Exp Cell Res 2010 May;316(8):1316-23

ELMOD2, a candidate gene for idiopathic pulmonary fibrosis, regulates antiviral responses.
Pulkkinen V, Bruce S, Rintahaka J, Hodgson U, Laitinen T, Alenius H, Kinnula VL, Myllärniemi M, Matikainen S, Kere J
FASEB J 2010 Apr;24(4):1167-77

Mechanisms of blast induced brain injuries, experimental studies in rats.
Risling M, Plantman S, Angeria M, Rostami E, Bellander BM, Kirkegaard M, Arborelius U, Davidsson J
Neuroimage 2011 Jan;54 Suppl 1():S89-97

Maturation of the adrenal medulla--IV. Effects of morphine.Formate assay in body fluids: application in methanol poisoning.
Anderson TR, Slotkin TA, Makar AB, McMartin KE, Palese M, Tephly TR
Biochem PharmacolBiochem Med 19751975 AugJun;2413(162):1469-74117-26

Gene expression profiling and chromatin immunoprecipitation identify DBN1, SETMAR and HIG2 as direct targets of SOX11 in mantle cell lymphoma.
Wang X, Björklund S, Wasik AM, Grandien A, Andersson P, Kimby E, Dahlman-Wright K, Zhao C, Christensson B, Sander B
PLoS One 2010 Nov;5(11):e14085

Global gene expression analysis of rodent motor neurons following spinal cord injury associates molecular mechanisms with development of postinjury spasticity.
Wienecke J, Westerdahl AC, Hultborn H, Kiehn O, Ryge J
J Neurophysiol 2010 Feb;103(2):761-78

Genome-wide characterisation of the Gcn5 histone acetyltransferase in budding yeast during stress adaptation reveals evolutionarily conserved and diverged roles.
Xue-Franzén Y, Johnsson A, Brodin D, Henriksson J, Bürglin TR, Wright AP
BMC Genomics 2010 Mar;11():200

Genome-wide mapping of estrogen receptor-beta-binding regions reveals extensive cross-talk with transcription factor activator protein-1.
Zhao C, Gao H, Liu Y, Papoutsi Z, Jaffrey S, Gustafsson JA, Dahlman-Wright K
Cancer Res 2010 Jun;70(12):5174-83