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.

Program director

Lauri Aaltonen
Tumor Genomics
Biomedicum 1
Haartmaninkatu 8
00014 University of Helsinki
tel. +358 2941 25595
lauri.aaltonen@helsinki.fi

Ralf Bützow
Outi Kilpivaara - Hematological Genetics
Anna Lepistö
Sirpa Leppä - Lymphoma Biology and Survival
Outi Monni - Oncogenomics
Päivi Pihlajamaa - Cancer Epimetabolism
Esa Pitkänen - Machine Learning in Biomedicine
Ari Ristimäki - Gastrointestinal Tumorigenesis
Biswajyoti Sahu - Enhancer Biology
Toni Seppälä
Jussi Taipale - Medical Systems Biology
Pia Vahteristo - Gynecological Tumor Genomics

Oskari Heikinheimo
Minna Pöyhönen
Laura Renkonen-Sinisalo
Ulla Wartiovaara-Kautto

Events

CancerBio Progress report seminar series
ATG Science Day, 6 October 2023

Key Publications from ATG

Sanjaya P, Maljanen K, Katainen R, Waszak SM; Genomics England Research Consortium; Aaltonen LA, Stegle O, Korbel JO, Pitkänen E. Mutation-Attention (MuAt): deep representation learning of somatic mutations for tumour typing and subtyping. Genome Med. 2023 Jul 7;15(1):47.
Hakkarainen M, Kaaja I, Douglas SPM, Vulliamy T, Dokal I, Soulier J, Larcher L, Peffault de Latour R, Leblanc T, Sicre de Fontbrune F, Siitonen T, Lohi O, Hellström-Lindberg E, Barbany G, Tesi B, Shimamura A, Beier F, Jackson S, Kuperman AA, Falik Zaccai T, Tamary H, Mecucci C, Capolsini I, Jahnukainen K, Salmenniemi U, Niinimäki R, Varilo T, Kilpivaara O*, Wartiovaara-Kautto U*. The Clinical Picture of the ERCC6L2 Disease - from Bone Marrow Failure to Acute Leukemia. Blood. 2023;141(23):2853-66.
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.