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Publications (original articles or review articles) published in 2022 from OUS - Department of Cancer Genetics

54 publications found

Ahearn TU, Zhang H, Michailidou K, Milne RL, Bolla MK, Dennis J, Dunning AM, Lush M, Wang Q, Andrulis IL, Anton-Culver H, Arndt V, Aronson KJ, Auer PL, Augustinsson A, Baten A, Becher H, Behrens S, Benitez J, Bermisheva M, Blomqvist C, Bojesen SE, Bonanni B, Børresen-Dale AL, Brauch H et al. (2022)
Common variants in breast cancer risk loci predispose to distinct tumor subtypes
Breast Cancer Res, 24 (1), 2
DOI 10.1186/s13058-021-01484-x, PubMed 34983606

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 (2022)
Plasma RNA profiling unveils transcriptional signatures associated with resistance to osimertinib in EGFR T790M positive non-small cell lung cancer patients
Transl Lung Cancer Res, 11 (10), 2064-2078
DOI 10.21037/tlcr-22-236, PubMed 36386450

Alver TN, Heintz KM, Hovig E, Bøe SL (2022)
Cooperative induction of receptor tyrosine kinases contributes to adaptive MAPK drug resistance in melanoma through the PI3K pathway
Cancer Rep (Hoboken), e1736 (in press)
DOI 10.1002/cnr2.1736, PubMed 36251678

Ambrosini M, Del Re M, Manca P, Hendifar A, Drilon A, Harada G, Ree AH, Klempner S, Mælandsmo GM, Flatmark K, Russnes HG, Cleary JM, Singh H, Sottotetti E, Martinetti A, Randon G, Sartore-Bianchi A, Capone I, Milione M, Di Bartolomeo M, Pietrantonio F (2022)
ALK Inhibitors in Patients With ALK Fusion-Positive GI Cancers: An International Data Set and a Molecular Case Series
JCO Precis Oncol, 6 (1), e2200015
DOI 10.1200/PO.22.00015, PubMed 35476549

Ankill J, Aure MR, Bjørklund S, Langberg S, Oslo Breast Cancer Consortium (OSBREAC) , Kristensen VN, Vitelli V, Tekpli X, Fleischer T (2022)
Epigenetic alterations at distal enhancers are linked to proliferation in human breast cancer
NAR Cancer, 4 (1), zcac008
DOI 10.1093/narcan/zcac008, PubMed 35350772

Athanasiadis P, Ianevski A, Skånland SS, Aittokallio T (2022)
Computational Pipeline for Rational Drug Combination Screening in Patient-Derived Cells
Methods Mol Biol, 2449, 327-348
DOI 10.1007/978-1-0716-2095-3_14, PubMed 35507270

Ballester PJ, Stevens R, Haibe-Kains B, Huang RS, Aittokallio T (2022)
Artificial intelligence for drug response prediction in disease models
Brief Bioinform, 23 (1)
DOI 10.1093/bib/bbab450, PubMed 34655289

Berg J, Halvorsen AR, Bengtson MB, Lindberg M, Halvorsen B, Aukrust P, Helland Å, Ueland T (2022)
Circulating T Cell Activation and Exhaustion Markers Are Associated With Radiation Pneumonitis and Poor Survival in Non-Small-Cell Lung Cancer
Front Immunol, 13, 875152
DOI 10.3389/fimmu.2022.875152, PubMed 35911763

Bergholtz H, Lien T, Lingaas F, Sørlie T (2022)
Comparative analysis of the molecular subtype landscape in canine and human mammary gland tumors
J Mammary Gland Biol Neoplasia, 27 (2), 171-183
DOI 10.1007/s10911-022-09523-9, PubMed 35932380

Bjørklund SS, Aure MR, Häkkinen J, Vallon-Christersson J, Kumar S, Evensen KB, Fleischer T, Tost J, OSBREAC, Sahlberg KK, Mathelier A, Bhanot G, Ganesan S, Tekpli X, Kristensen VN (2022)
Subtype and cell type specific expression of lncRNAs provide insight into breast cancer
Commun Biol, 5 (1), 834
DOI 10.1038/s42003-022-03559-7, PubMed 35982125

Børø S, Thoresen S, Helland Å (2022)
Improvements in survival for patients with stage IV adenocarcinoma in the lung, diagnosed between 2010 - 2020 - A population-based registry study from Norway
Front Oncol, 12, 1017902
DOI 10.3389/fonc.2022.1017902, PubMed 36523970

Callesen LB, Hamfjord J, Boysen AK, Pallisgaard N, Guren TK, Kure EH, Spindler KG (2022)
Circulating tumour DNA and its clinical utility in predicting treatment response or survival in patients with metastatic colorectal cancer: a systematic review and meta-analysis
Br J Cancer, 127 (3), 500-513
DOI 10.1038/s41416-022-01816-4, PubMed 35440666

Callesen LB, Takacova T, Hamfjord J, Würschmidt F, Oldhafer KJ, Brüning R, Arnold D, Spindler KG (2022)
Circulating DNA in patients undergoing loco-regional treatment of colorectal cancer metastases: a systematic review and meta-analysis
Ther Adv Med Oncol, 14, 17588359221133171
DOI 10.1177/17588359221133171, PubMed 36339929

Castro-Mondragon JA, Aure MR, Lingjærde OC, Langerød A, Martens JWM, Børresen-Dale AL, Kristensen VN, Mathelier A (2022)
Cis-regulatory mutations associate with transcriptional and post-transcriptional deregulation of gene regulatory programs in cancers
Nucleic Acids Res, 50 (21), 12131-48 (in press)
DOI 10.1093/nar/gkac1143, PubMed 36477895

Chen J, Song Y, Li Y, Wei Y, Shen S, Zhao Y, You D, Su L, Bjaanaes MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Shen H, Christiani DC, Zhang R, Chen F (2022)
A trans-omics assessment of gene-gene interaction in early-stage NSCLC
Mol Oncol, 17 (1), 173-187
DOI 10.1002/1878-0261.13345, PubMed 36408734

Denisova OV, Merisaari J, Kaur A, Yetukuri L, Jumppanen M, von Schantz-Fant C, Ohlmeyer M, Wennerberg K, Aittokallio T, Taipale M, Westermarck J (2022)
Development of actionable targets of multi-kinase inhibitors (AToMI) screening platform to dissect kinase targets of staurosporines in glioblastoma cells
Sci Rep, 12 (1), 13796
DOI 10.1038/s41598-022-18118-7, PubMed 35963891

Dorraji E, Borgen E, Segura-Peña D, Rawat P, Smorodina E, Dunn C, Greiff V, Sekulić N, Russnes H, Kyte JA (2022)
Development of a High-Affinity Antibody against the Tumor-Specific and Hyperactive 611-p95HER2 Isoform
Cancers (Basel), 14 (19)
DOI 10.3390/cancers14194859, PubMed 36230782

Eide IJZ, Stensgaard S, Helland Å, Ekman S, Mellemgaard A, Hansen KH, Cicenas S, Koivunen J, Grønberg BH, Sørensen BS, Brustugun OT (2022)
Osimertinib in non-small cell lung cancer with uncommon EGFR-mutations: a post-hoc subgroup analysis with pooled data from two phase II clinical trials
Transl Lung Cancer Res, 11 (6), 953-963
DOI 10.21037/tlcr-21-995, PubMed 35832438

Eliseussen E, Fleischer T, Vitelli V (2022)
Rank-based Bayesian variable selection for genome-wide transcriptomic analyses
Stat Med, 41 (23), 4532-4553
DOI 10.1002/sim.9524, PubMed 35844145

Flobak Å, Skånland SS, Hovig E, Taskén K, Russnes HG (2022)
Functional precision cancer medicine: drug sensitivity screening enabled by cell culture models
Trends Pharmacol Sci, 43 (11), 973-985
DOI 10.1016/j.tips.2022.08.009, PubMed 36163057

Girard N, Bar J, Garrido P, Garassino MC, McDonald F, Mornex F, Filippi AR, Smit HJM, Peters S, Field JK, Christoph DC, Sibille A, Fietkau R, Haakensen VD, Chouaid C, Markman B, Hiltermann TJN, Taus A, Sawyer W, Allen A, Chander P, Licour M, Solomon B (2022)
Treatment Characteristics and Real-World Progression-Free Survival in Patients With Unresectable Stage III NSCLC Who Received Durvalumab After Chemoradiotherapy: Findings From the PACIFIC-R Study
J Thorac Oncol, 18 (2), 181-193
DOI 10.1016/j.jtho.2022.10.003, PubMed 36307040

Halkola AS, Aittokallio T, Parvinen K (2022)
Tumor microenvironment as a metapopulation model: The effects of angiogenesis, emigration and treatment modalities
J Theor Biol, 545, 111147
DOI 10.1016/j.jtbi.2022.111147, PubMed 35489642

Helland Å, Andersen KK, Myklebust TÅ, Johannesen TB, Aarøe J, Enerly E (2022)
EGFR-mutation testing and TKI treatment patterns in locally advanced and metastatic NSCLC in Norway - A nationwide retrospective cohort study
Cancer Treat Res Commun, 33, 100636
DOI 10.1016/j.ctarc.2022.100636, PubMed 36155129

Helland Å, Russnes HG, Fagereng GL, Al-Shibli K, Andersson Y, Berg T, Bjørge L, Blix E, Bjerkehagen B, Brabrand S, Cameron MG, Dalhaug A, Dietzel D, Dønnem T, Enerly E, Flobak Å, Fluge S, Gilje B, Gjertsen BT, Grønberg BH, Grønås K, Guren T, Hamre H, Haug Å, Heinrich D et al. (2022)
Improving public cancer care by implementing precision medicine in Norway: IMPRESS-Norway
J Transl Med, 20 (1), 225
DOI 10.1186/s12967-022-03432-5, PubMed 35568909

Hjerkind KV, Johansson ALV, Trewin CB, Russnes HG, Ursin G (2022)
Incidence of breast cancer subtypes in immigrant and non-immigrant women in Norway
Breast Cancer Res, 24 (1), 4
DOI 10.1186/s13058-021-01498-5, PubMed 35012613

Horndalsveen H, Alver TN, Dalsgaard AM, Rogg LV, Helbekkmo N, Grønberg BH, Halvorsen TO, Ramberg C, Haakensen VD, Öjlert ÅK, Bjaanaes MM, Helland Å (2022)
Atezolizumab and stereotactic body radiotherapy in patients with advanced non-small cell lung cancer: safety, clinical activity and ctDNA responses-the ComIT-1 trial
Mol Oncol (in press)
DOI 10.1002/1878-0261.13330, PubMed 36330681

Ianevski A, Giri AK, Aittokallio T (2022)
Fully-automated and ultra-fast cell-type identification using specific marker combinations from single-cell transcriptomic data
Nat Commun, 13 (1), 1246
DOI 10.1038/s41467-022-28803-w, PubMed 35273156

Ianevski A, Giri AK, Aittokallio T (2022)
SynergyFinder 3.0: an interactive analysis and consensus interpretation of multi-drug synergies across multiple samples
Nucleic Acids Res, 50 (W1), W739-43 (in press)
DOI 10.1093/nar/gkac382, PubMed 35580060

Ji X, Lin L, Fan J, Li Y, Wei Y, Shen S, Su L, Shafer A, Bjaanaes MM, Karlsson A, Planck M, Staaf J, Helland Å, Esteller M, Zhang R, Chen F, Christiani DC (2022)
Epigenome-wide three-way interaction study identifies a complex pattern between TRIM27, KIAA0226, and smoking associated with overall survival of early-stage NSCLC
Mol Oncol, 16 (3), 717-731
DOI 10.1002/1878-0261.13167, PubMed 34932879

Khadse A, Haakensen VD, Silwal-Pandit L, Hamfjord J, Micke P, Botling J, Brustugun OT, Lingjærde OC, Helland Å, Kure EH (2022)
Prognostic Significance of the Loss of Heterozygosity of KRAS in Early-Stage Lung Adenocarcinoma
Front Oncol, 12, 873532
DOI 10.3389/fonc.2022.873532, PubMed 35574381

Kong W, He L, Zhu J, Brück O, Porkka K, Heckman CA, Zhu S, Aittokallio T (2022)
An immunity and pyroptosis gene-pair signature predicts overall survival in acute myeloid leukemia
Leukemia, 36 (10), 2384-2395
DOI 10.1038/s41375-022-01662-6, PubMed 35945345

Kong W, Midena G, Chen Y, Athanasiadis P, Wang T, Rousu J, He L, Aittokallio T (2022)
Systematic review of computational methods for drug combination prediction
Comput Struct Biotechnol J, 20, 2807-2814
DOI 10.1016/j.csbj.2022.05.055, PubMed 35685365

Kosibaty Z, Brustugun OT, Zwicky Eide IJ, Tsakonas G, Grundberg O, De Petris L, McGowan M, Hydbring P, Ekman S (2022)
Ras-Related Protein Rab-32 and Thrombospondin 1 Confer Resistance to the EGFR Tyrosine Kinase Inhibitor Osimertinib by Activating Focal Adhesion Kinase in Non-Small Cell Lung Cancer
Cancers (Basel), 14 (14)
DOI 10.3390/cancers14143430, PubMed 35884490

Langille E, Al-Zahrani KN, Ma Z, Liang M, Uuskula-Reimand L, Espin R, Teng K, Malik A, Bergholtz H, Ghamrasni SE, Afiuni-Zadeh S, Tsai R, Alvi S, Elia A, Lü Y, Oh RH, Kozma KJ, Trcka D, Narimatsu M, Liu JC, Nguyen T, Barutcu S, Loganathan SK, Bremner R, Bader GD et al. (2022)
Loss of Epigenetic Regulation Disrupts Lineage Integrity, Induces Aberrant Alveogenesis, and Promotes Breast Cancer
Cancer Discov, 12 (12), 2930-2953
DOI 10.1158/2159-8290.CD-21-0865, PubMed 36108220

Lemma RB, Fleischer T, Martinsen E, Ledsaak M, Kristensen V, Eskeland R, Gabrielsen OS, Mathelier A (2022)
Pioneer transcription factors are associated with the modulation of DNA methylation patterns across cancers
Epigenetics Chromatin, 15 (1), 13
DOI 10.1186/s13072-022-00444-9, PubMed 35440061

Lobert VH, Skardal ML, Malerød L, Simensen JE, Algra HA, Andersen AN, Fleischer T, Enserink HA, Liestøl K, Heath JK, Rusten TE, Stenmark HA (2022)
PHLPP1 regulates CFTR activity and lumen expansion through AMPK
Development, 149 (20)
DOI 10.1242/dev.200955, PubMed 35997536

Maggadóttir SM, Kvalheim G, Wernhoff P, Sæbøe-Larssen S, Revheim ME, Josefsen D, Wälchli S, Helland Å, Inderberg EM (2022)
A phase I/II escalation trial design T-RAD: Treatment of metastatic lung cancer with mRNA-engineered T cells expressing a T cell receptor targeting human telomerase reverse transcriptase (hTERT)
Front Oncol, 12, 1031232
DOI 10.3389/fonc.2022.1031232, PubMed 36439452

Mo T, Brandal SHB, Köhn-Luque A, Engebraaten O, Kristensen VN, Fleischer T, Hompland T, Seierstad T (2022)
Quantification of Tumor Hypoxia through Unsupervised Modelling of Consumption and Supply Hypoxia MR Imaging in Breast Cancer
Cancers (Basel), 14 (5)
DOI 10.3390/cancers14051326, PubMed 35267636

Murumägi A, Ungureanu D, Khan S, Arjama M, Välimäki K, Ianevski A, Ianevski P, Bergström R, Dini A, Kanerva A, Koivisto-Korander R, Tapper J, Lassus H, Loukovaara M, Mägi A, Hirasawa A, Aoki D, Pietiäinen V, Pellinen T, Bützow R, Aittokallio T, Kallioniemi O (2022)
Drug response profiles in patient-derived cancer cells across histological subtypes of ovarian cancer: real-time therapy tailoring for a patient with low-grade serous carcinoma
Br J Cancer (in press)
DOI 10.1038/s41416-022-02067-z, PubMed 36476658

Pedersen CA, Cao MD, Fleischer T, Rye MB, Knappskog S, Eikesdal HP, Lønning PE, Tost J, Kristensen VN, Tessem MB, Giskeødegård GF, Bathen TF (2022)
DNA methylation changes in response to neoadjuvant chemotherapy are associated with breast cancer survival
Breast Cancer Res, 24 (1), 43
DOI 10.1186/s13058-022-01537-9, PubMed 35751095

Ravindran V, Wagoner J, Athanasiadis P, Den Hartigh AB, Sidorova JM, Ianevski A, Fink SL, Frigessi A, White J, Polyak SJ, Aittokallio T (2022)
Discovery of host-directed modulators of virus infection by probing the SARS-CoV-2-host protein-protein interaction network
Brief Bioinform, 23 (6)
DOI 10.1093/bib/bbac456, PubMed 36305426

Ree AH, Mælandsmo GM, Flatmark K, Russnes HG, Gómez Castañeda M, Aas E (2022)
Cost-effectiveness of molecularly matched off-label therapies for end-stage cancer - the MetAction precision medicine study
Acta Oncol, 61 (8), 955-962
DOI 10.1080/0284186X.2022.2098053, PubMed 35943168

Seborova K, Hlavac V, Holy P, Bjørklund SS, Fleischer T, Rob L, Hruda M, Bouda J, Mrhalova M, Allah MMKAO, Vodicka P, Fiala O, Soucek P, Kristensen VN, Vodickova L, Vaclavikova R (2022)
Complex molecular profile of DNA repair genes in epithelial ovarian carcinoma patients with different sensitivity to platinum-based therapy
Front Oncol, 12, 1016958
DOI 10.3389/fonc.2022.1016958, PubMed 36531044

Silwal-Pandit L, Stålberg SM, Henrik J. Johansson, Georgios Mermelekas, Lothe IMB, Skrede ML, Dalsgaard AM, Nebdal D, Helland, Lingjærde OC, Labori KJ, Skålhegg BS, Janne Lehtiö, Kure EH (2022)
Proteome Analysis of Pancreatic Tumors Implicates Extracellular Matrix in Patient Outcome
Cancer Res Commun, 2 (6), 434-446
DOI 10.1158/2767-9764.CRC-21-0100, PublikaID 411

Smirnov P, Smith I, Safikhani Z, Ba-Alawi W, Khodakarami F, Lin E, Yu Y, Martin S, Ortmann J, Aittokallio T, Hafner M, Haibe-Kains B (2022)
Evaluation of statistical approaches for association testing in noisy drug screening data
BMC Bioinformatics, 23 (1), 188
DOI 10.1186/s12859-022-04693-z, PubMed 35585485

Staaf J, Häkkinen J, Hegardt C, Saal LH, Kimbung S, Hedenfalk I, Lien T, Sørlie T, Naume B, Russnes H, Marcone R, Ayyanan A, Brisken C, Malterling RR, Asking B, Olofsson H, Lindman H, Bendahl PO, Ehinger A, Larsson C, Loman N, Rydén L, Malmberg M, Borg Å, Vallon-Christersson J (2022)
RNA sequencing-based single sample predictors of molecular subtype and risk of recurrence for clinical assessment of early-stage breast cancer
NPJ Breast Cancer, 8 (1), 94
DOI 10.1038/s41523-022-00465-3, PubMed 35974007

Umu SU, Langseth H, Zuber V, Helland Å, Lyle R, Rounge TB (2022)
Serum RNAs can predict lung cancer up to 10 years prior to diagnosis
Elife, 11
DOI 10.7554/eLife.71035, PubMed 35147498

Vitelli V, Fleischer T, Ankill J, Arjas E, Frigessi A, Kristensen VN, Zucknick M (2022)
Transcriptomic pan-cancer analysis using rank-based Bayesian inference
Mol Oncol (in press)
DOI 10.1002/1878-0261.13354, PubMed 36562628

Wang T, Pulkkinen OI, Aittokallio T (2022)
Target-specific compound selectivity for multi-target drug discovery and repurposing
Front Pharmacol, 13, 1003480
DOI 10.3389/fphar.2022.1003480, PubMed 36225560

Wolf J, Helland Å, Oh IJ, Migliorino MR, Dziadziuszko R, Wrona A, de Castro J, Mazieres J, Griesinger F, Chlistalla M, Cardona A, Ruf T, Trunzer K, Smoljanovic V, Novello S (2022)
Final efficacy and safety data, and exploratory molecular profiling from the phase III ALUR study of alectinib versus chemotherapy in crizotinib-pretreated ALK-positive non-small-cell lung cancer
ESMO Open, 7 (1), 100333
DOI 10.1016/j.esmoop.2021.100333, PubMed 35042152

Wolowczyk C, Neckmann U, Aure MR, Hall M, Johannessen B, Zhao S, Skotheim RI, Andersen SB, Zwiggelaar R, Steigedal TS, Lingjærde OC, Sahlberg KK, Almaas E, Bjørkøy G (2022)
NRF2 drives an oxidative stress response predictive of breast cancer
Free Radic Biol Med, 184, 170-184
DOI 10.1016/j.freeradbiomed.2022.03.029, PubMed 35381325

Yin Y, Athanasiadis P, Karlsen L, Urban A, Xu H, Murali I, Fernandes SM, Arribas AJ, Hilli AK, Taskén K, Bertoni F, Mato AR, Normant E, Brown JR, Tjønnfjord GE, Aittokallio T, Skånland SS (2022)
Functional Testing to Characterize and Stratify PI3K Inhibitor Responses in Chronic Lymphocytic Leukemia
Clin Cancer Res, 28 (20), 4444-4455
DOI 10.1158/1078-0432.CCR-22-1221, PubMed 35998013

Zhao Z, Wang S, Zucknick M, Aittokallio T (2022)
Tissue-specific identification of multi-omics features for pan-cancer drug response prediction
iScience, 25 (8), 104767
DOI 10.1016/j.isci.2022.104767, PubMed 35992090

Zhao Z, Zucknick M, Aittokallio T (2022)
EnrichIntersect: an R package for custom set enrichment analysis and interactive visualization of intersecting sets
Bioinform Adv, 2 (1), vbac073
DOI 10.1093/bioadv/vbac073, PubMed 36699400