Applied Tumor Genomics Research (ATG)
Applied Tumor Genomics Research Program aims to advance the understanding of the genetic and environmental signals that lead to neoplasia: improving the knowledge of the function of the coding and noncoding genome, exploiting the public data, and creating and analyzing new key data sets from highly selected patient populations.
- Oskari Heikinheimo
- Minna Pöyhönen
- Laura Renkonen-Sinisalo
- Ulla Wartiovaara-Kautto
Key Publications from ATG
- Sahu B, Hartonen T, Pihlajamaa P, Wei B, Dave K, Zhu F, Kaasinen E, Lidschreiber K, Lidschreiber M, Daub CO, Cramer P, Kivioja T & Taipale J. Sequence determinants of human gene regulatory elements. Nat Genet 54, 283–294 (2022).
- Kuisma H, Bramante S, Rajamäki K, Sipilä LJ, Kaasinen E, Kaukomaa J, Palin K, Mäkinen N, Sjöberg J, Sarvilinna N, Taipale J, Kauppi L, Tumiati M, Hassinen A, Pitkäniemi J, Jalkanen J, Heikkinen S, Pasanen A, Heikinheimo O, Bützow R, Välimäki N & Aaltonen LA. Parity associates with chromosomal damage in uterine leiomyomas. Nature Communications. 12, 1, 5448, Sep 2021.
- Berta DG, Kuisma H, Välimäki N, Räisänen M, Jäntti M, Pasanen A, Karhu A, Kaukomaa J, Taira A, Cajuso T, Nieminen S, Penttinen R-M, Ahonen S, Lehtonen R, Mehine M, Vahteristo P, Jalkanen J, Sahu B, Ravantti J, Mäkinen N, Rajamäki K, Palin K, Taipale J, Heikinheimo O, Bützow R, Kaasinen E & Aaltonen LA. Deficient H2A.Z deposition is associated with genesis of uterine leiomyoma. Nature 596, 398-403, 2021.
- Sahu B, Pihlajamaa P, Zhang K, Palin K, Ahonen S, Cervera A, Ristimäki A, Aaltonen LA, Hautaniemi S & Taipale J. Human cell transformation by combined lineage conversion and oncogene expression. Oncogene 40, 5533–5547 (2021).
- Rajamäki K, Taira A, Katainen R, Välimäki N, Kuosmanen A, Plaketti R-M, Seppälä TT, Ahtiainen M, Wirta E-V, Vartiainen E, Sulo P, Ravantti J, Suvi Lehtipuro S, Granberg K, Nykter M, Tanskanen T, Ristimäki A, Koskensalo S, Renkonen-Sinisalo L, Lepistö A, Böhm J, Taipale J, Mecklin J-P, Aavikko M, Palin K & Aaltonen LA. Genetic and epigenetic characteristics of inflammatory bowel disease associated colorectal cancer. Gastroenterology 161:2, 592-607, Aug 2021.
- Mehine M, Khamaiseh S, Ahvenainen T, Heikkinen T, Äyräväinen A, Pakarinen P, Härkki P, Pasanen A, Bützow R, Vahteristo P. 3´RNA sequencing accurately classifies formalin-fixed paraffin-embedded uterine leiomyomas. Cancers, 2020, 12:3839.
- Holm M, Andersson E, Osterlund E, Ovissi A, Soveri LM, Anttonen AK, Kytölä S, Aittomäki K, Österlund P, Ristimäki A. Detection of KRAS mutations in liquid biopsies from metastatic colorectal cancer patients using droplet digital PCR, Idylla, and next generation sequencing. PlosOne, 2020, 15(11).
- Karvonen H, Arjama M, Kaleva L, Niininen W, Barker H, Koivisto-Korander R, Tapper J, Pakarinen P, Lassus H, Loukovaara M, Bützow R, Kallioniemi O, Murumägi A and Ungureanu D. Glucocorticoids induce differentiation and chemoresistance in ovarian cancer by promoting ROR1-mediated stemness. Cell Death and Disease, 2020, 11(9):790.
- Dziubańska-Kusibab PJ, Berger H, Battistini F, Bouwman B.A.M., Iftekhar A, Katainen R, Cajuso T, Crosetto N, Orozco M, Aaltonen LA & Meyer TF. Colibactin DNA-damage signature indicates mutational impact in colorectal cancer. Nature Medicine, 2020, 26:1063-1069.
- Pasanen A, Ahvenainen T, Pellinen T, Vahteristo P, Loukovaara M, Bützow R. PD-L1 expression in endometrial carcinoma cells and intratumoral immune cells: differences across histologic and TCGA-based molecular subgroups. American Journal of Surgical Pathology, 2020, 44(2):174-181.
- ICGC/TCGA Pan-Cancer Analysis of Whole Genomes Consortium (a large number of contributors, including members from the Aaltonen & Pitkänen group). Pan-cancer analysis of whole genomes. Nature, 2020, 578:82-93.
- Quist-Paulsen P, Toft N , Heyman M, Abrahamsson J, Griškevičius J, Hallböök H, Jónsson ÓG, Palk K, Pruunsild K, Vaitkeviciene G, Vettenranta K, Åsberg A1, Frandsen TL, Opdahl S, Marquart HV, Madsen HO, Overgaard UM, Wartiovaara-Kautto U, Schmiegelow K. T cell acute lymphoblastic leukemia in patients 1-45 years treated with the pediatric NOPHO ALL2008 protocol. Leukemia, 2020, 34(2):347-357.
- Äyräväinen A, Pasanen A, Ahvenainen T, Heikkinen T, Pakarinen P, Härkki P, Vahteristo P. Systematic molecular and clinical analysis of uterine leiomyomas from fertile-aged women undergoing myomectomy. Human Reproduction, 2020, deaa187:1–17.
- Kaasinen E, Kuismin O, Rajamäki K, Ristolainen H, Aavikko M, Kondelin J, Saarinen S, Berta D, Katainen R, Hirvonen E, Karhu A, Taira A, Tanskanen T, Alkodsi A, Taipale M, Morgunova E, Franssila K, Lehtonen R, Mäkinen M, Aittomäki K, Palotie A, Kurki M, Pietiläinen O, Hilpert M, Saarentaus E, Niinimäki J, Junttila J, Kaikkonen K, Vahteristo P, Skoda R, Seppänen M, Eklund K, Taipale J, Kilpivaara O* & Aaltonen LA*. Impact of Constitutional TET2 Haploinsufficiency on Molecular and Clinical Phenotype in Humans. Nature Communications, 2019, 10:1252. *equal contribution
- Cajuso T, Sulo P, Tanskanen T, Katainen R, Taira A, Hänninen U, Kondelin J, Forsström L, Välimäki N, Aavikko M, Kaasinen E, Ristimäki, Koskensalo S, Lepistö A, Renkonen-Sinisalo L, Seppälä T, Kuopio T, Böhm J, Mecklin J-P, Kilpivaara O, Pitkänen E, Palin K & Aaltonen LA. Retrotransposon insertions can initiate colorectal cancer and are associated with poor survival. Nature Communications, 2019, 10:4022.
- Olkinuora A, Nieminen TT, Mårtensson E, Rohlin A, Ristimäki A, Koskenvuo L, Lepistö A; Swedish Extended Genetic Analysis of Colorectal Neoplasia (SWEN) Study Group, Gebre-Medhin S, Nordling M, Peltomäki P. Biallelic germline nonsense variant of MLH3 underlies polyposis predisposition. Genet Med, 2019, 21:1868-1873.
- Tuomainen K, Al-Samadi A, Potdar S, Turunen L, Turunen M, Karhemo PR, Bergman P, Risteli M, Åström P, Tiikkaja R, Grenman R, Wennerberg K, Monni O, Salo T. Human Tumor-Derived Matrix Improves the Predictability of Head and Neck Cancer Drug Testing. Cancers (Basel), 2019, 12(1), pii: E92.
- Karjalainen EK, Renkonen-Sinisalo L, Mustonen HK, Lepistö AH. Morbidity related to diverting ileostomy after restorative proctocolectomy in patients with ulcerative colitis. Colorectal Disease, 2019, 21(6):671-678.
- Douglas S.P.M, Siipola P, Kovanen P.E., Pyörälä M, Kakko S, Savolainen E-R, Salmenniemi U, Orte K, Kytölä S, Pitkänen E, Porkka K, Kilpivaara O,* Wartiovaara-Kautto U*. ERCC6L2 defines a novel entity within inherited acute myeloid leukemia Blood, 2019, 133(25):2724-2728. *equal contribution
- Hirvonen EAM, Peuhkuri S, Norberg A, Degerman S, Hannula-Jouppi K, Välimaa H, Kilpivaara O*, Wartiovaara-Kautto U*. Characterization of an X-chromosome-linked telomere biology disorder in females with DKC1 mutation. Leukemia, 2019, 33(1):275-278. *equal contribution
- Leivonen S-K, Pollari M, Brück O, Pellinen T, Autio M, Vähämurto P, Karjalainen-Lindsberg M-L, Mannisto S, Kellokumpu-Lehtinen P-L, Mustjoki S, Leppä S. T-cell inflamed tumor microenvironment predicts favorable prognosis in primary testicular lymphoma. Haematologica, 2019, 104(2):338-346.
- Göös H, Fogarty C.L, Sahu B, Plagnol V, Rajamäki K, Nurmi K, Liu X, Einarsdottir E, Jouppila A, Pettersson T, Vihinen H, Krjutskov K, Saavalainen P, Järvinen A, Muurinen M, Greco D, Scala G, Curtis J, Nordström D, Flaumenhaft R, Vaarala O, Kovanen P.E, Keskitalo S, Ranki A, Kere J, Lehto M, Notarangelo L.D, Nejentsev S, Eklund K.K, Varjosalo M, Taipale J, Seppanen M.R. J. / Gain-of-function CEBPE mutation causes noncanonical autoinflammatory inflammasomopathy. Journal of Allergy and Clinical Immunology. 2019, 144(5):1364-1376.