1
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Kallio HM, Savolainen K, Virtanen T, Ryyppö L, Selin H, Martikainen P, Staff S, Kivinummi K, Sipola J, Vuorinen J, Nikkola J, Nykter M, Auranen A, Annala M. Sensitive circulating tumor DNA-based residual disease detection in epithelial ovarian cancer. Life Sci Alliance 2024; 7:e202402658. [PMID: 38580393 PMCID: PMC10997860 DOI: 10.26508/lsa.202402658] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2024] [Revised: 03/15/2024] [Accepted: 03/18/2024] [Indexed: 04/07/2024] Open
Abstract
Epithelial ovarian cancer (EOC) is one of the leading causes of cancer-related death in women worldwide, and is characterized by a high rate of recurrence after surgery and chemotherapy. We sought to implement a circulating tumor DNA (ctDNA)-based blood test for more accurate post-operative surveillance of this disease. We analyzed 264 plasma samples collected between June 2016 and September 2021 from 63 EOC patients using tumor-guided plasma cell-free DNA analysis to detect residual disease after treatment. Assay specificity was verified using cross-patient analysis of 1,195 control samples. ctDNA was detected in 51 of 55 (93%) samples at diagnosis, and 18 of 18 (100%) samples at progression. Positive ctDNA in the last on-treatment sample was associated with rapid progression (median 1.02 versus 3.38 yr, HR = 5.63, P < 0.001) and reduced overall survival (median 2.31 versus NR yr, HR = 8.22, P < 0.001) in patients with high-grade serous cancer. In the case of 12 patients, ctDNA assays detected progression earlier than standard surveillance, with a median lead time of 5.9 mo. To approach the physical limits of ctDNA detection, five patients were analyzed using ultra-sensitive assays interrogating 479-1,856 tumor mutations, capable of tracking ctDNA fractions down to 0.0004%. Our results demonstrate that ctDNA assays achieve high sensitivity and specificity in detecting post-operative residual disease in EOC.
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Affiliation(s)
- Heini Ml Kallio
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Kalle Savolainen
- https://ror.org/02hvt5f17 Department of Obstetrics and Gynecology, Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Tuomo Virtanen
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Lauri Ryyppö
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Hanna Selin
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Päivi Martikainen
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Synnöve Staff
- https://ror.org/02hvt5f17 Department of Obstetrics and Gynecology, Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Kati Kivinummi
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Joonatan Sipola
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Juuso Vuorinen
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Jussi Nikkola
- https://ror.org/02hvt5f17 Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Annika Auranen
- https://ror.org/02hvt5f17 Department of Obstetrics and Gynecology, Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
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2
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Hartewig A, Huhtala L, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Rautajoki KJ. Aberrant DNA methylation distorts developmental trajectories in atypical teratoid/rhabdoid tumors. Life Sci Alliance 2024; 7:e202302088. [PMID: 38499326 PMCID: PMC10948937 DOI: 10.26508/lsa.202302088] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/11/2023] [Revised: 03/06/2024] [Accepted: 03/06/2024] [Indexed: 03/20/2024] Open
Abstract
Atypical teratoid/rhabdoid tumors (AT/RTs) are pediatric brain tumors known for their aggressiveness and aberrant but still unresolved epigenetic regulation. To better understand their malignancy, we investigated how AT/RT-specific DNA hypermethylation was associated with gene expression and altered transcription factor binding and how it is linked to upstream regulation. Medulloblastomas, choroid plexus tumors, pluripotent stem cells, and fetal brain were used as references. A part of the genomic regions, which were hypermethylated in AT/RTs similarly as in pluripotent stem cells and demethylated in the fetal brain, were targeted by neural transcriptional regulators. AT/RT-unique DNA hypermethylation was associated with polycomb repressive complex 2 and linked to suppressed genes with a role in neural development and tumorigenesis. Activity of the several NEUROG/NEUROD pioneer factors, which are unable to bind to methylated DNA, was compromised via the suppressed expression or DNA hypermethylation of their target sites, which was also experimentally validated for NEUROD1 in medulloblastomas and AT/RT samples. These results highlight and characterize the role of DNA hypermethylation in AT/RT malignancy and halted neural cell differentiation.
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Affiliation(s)
- Meeri Pekkarinen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kristiina Nordfors
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Unit of Pediatric Hematology and Oncology, Tampere University Hospital, Tampere, Finland
| | - Joonas Uusi-Mäkelä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ville Kytölä
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Laura Huhtala
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Minna Rauhala
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Henna Urhonen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Sergei Häyrynen
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Ebrahim Afyounian
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Olli Yli-Harja
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Pauli Helen
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Olli Lohi
- https://ror.org/033003e23 Tampere Center for Child Health Research, Tays Cancer Center, Tampere University and Tampere University Hospital, Tampere, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Hannu Haapasalo
- https://ror.org/033003e23 Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Department of Neurosurgery, Tays Cancer Centre, Tampere University Hospital and Tampere University, Tampere, Finland
- https://ror.org/031y6w871 Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Rautajoki
- https://ror.org/033003e23 Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- https://ror.org/033003e23 Tampere Institute for Advanced Study, Tampere University, Tampere, Finland
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3
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Fonseca NM, Maurice-Dror C, Herberts C, Tu W, Fan W, Murtha AJ, Kollmannsberger C, Kwan EM, Parekh K, Schönlau E, Bernales CQ, Donnellan G, Ng SWS, Sumiyoshi T, Vergidis J, Noonan K, Finch DL, Zulfiqar M, Miller S, Parimi S, Lavoie JM, Hardy E, Soleimani M, Nappi L, Eigl BJ, Kollmannsberger C, Taavitsainen S, Nykter M, Tolmeijer SH, Boerrigter E, Mehra N, van Erp NP, De Laere B, Lindberg J, Grönberg H, Khalaf DJ, Annala M, Chi KN, Wyatt AW. Prediction of plasma ctDNA fraction and prognostic implications of liquid biopsy in advanced prostate cancer. Nat Commun 2024; 15:1828. [PMID: 38418825 PMCID: PMC10902374 DOI: 10.1038/s41467-024-45475-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 01/24/2024] [Indexed: 03/02/2024] Open
Abstract
No consensus strategies exist for prognosticating metastatic castration-resistant prostate cancer (mCRPC). Circulating tumor DNA fraction (ctDNA%) is increasingly reported by commercial and laboratory tests but its utility for risk stratification is unclear. Here, we intersect ctDNA%, treatment outcomes, and clinical characteristics across 738 plasma samples from 491 male mCRPC patients from two randomized multicentre phase II trials and a prospective province-wide blood biobanking program. ctDNA% correlates with serum and radiographic metrics of disease burden and is highest in patients with liver metastases. ctDNA% strongly predicts overall survival, progression-free survival, and treatment response independent of therapeutic context and outperformed established prognostic clinical factors. Recognizing that ctDNA-based biomarker genotyping is limited by low ctDNA% in some patients, we leverage the relationship between clinical prognostic factors and ctDNA% to develop a clinically-interpretable machine-learning tool that predicts whether a patient has sufficient ctDNA% for informative ctDNA genotyping (available online: https://www.ctDNA.org ). Our results affirm ctDNA% as an actionable tool for patient risk stratification and provide a practical framework for optimized biomarker testing.
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Affiliation(s)
- Nicolette M Fonseca
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Wilson Tu
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - William Fan
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Andrew J Murtha
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | | | - Edmond M Kwan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
- Department of Medicine, School of Clinical Sciences; Monash University, Melbourne, VIC, Australia
| | - Karan Parekh
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elena Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Cecily Q Bernales
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Gráinne Donnellan
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Takayuki Sumiyoshi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Urology, Graduate School of Medicine, Kyoto University, Kyoto, Japan
| | - Joanna Vergidis
- Department of Medical Oncology, BC Cancer, Victoria, BC, Canada
| | - Krista Noonan
- Department of Medical Oncology, BC Cancer, Surrey, BC, Canada
| | - Daygen L Finch
- Department of Medical Oncology, BC Cancer, Kelowna, BC, Canada
| | | | - Stacy Miller
- Department of Radiation Oncology, BC Cancer, Prince George, BC, Canada
| | - Sunil Parimi
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Edward Hardy
- Tom McMurtry & Peter Baerg Cancer Centre, Vernon Jubilee Hospital, Vernon, BC, Canada
| | - Maryam Soleimani
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Lucia Nappi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Bernhard J Eigl
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | | | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Sofie H Tolmeijer
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Emmy Boerrigter
- Department of Pharmacy, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Niven Mehra
- Department of Medical Oncology, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Nielka P van Erp
- Department of Pharmacy, Research Institute for Medical Innovation, Radboud University, Nijmegen, The Netherlands
| | - Bram De Laere
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
- Cancer Research Institute Ghent (CRIG), Ghent University, Ghent, Belgium
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Johan Lindberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Henrik Grönberg
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Daniel J Khalaf
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada.
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
- Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, BC, Canada.
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4
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Kivioja T, Posti JP, Sipilä J, Rauhala M, Frantzén J, Gardberg M, Rahi M, Rautajoki K, Nykter M, Vuorinen V, Nordfors K, Haapasalo H, Haapasalo J. Motor dysfunction as a primary symptom predicts poor outcome: multicenter study of glioma symptoms. Front Oncol 2024; 13:1305725. [PMID: 38239655 PMCID: PMC10794640 DOI: 10.3389/fonc.2023.1305725] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2023] [Accepted: 11/27/2023] [Indexed: 01/22/2024] Open
Abstract
Background and objectives The objectives of this study were to investigate the prognostic value of primary symptoms and leading symptoms in adult patients with diffuse infiltrating glioma and to provide a clinical perspective for evaluating survival. Methods This study included a retrospective cohort from two tertiary university hospitals (n = 604, 2006-2013, Tampere University Hospital and Turku University Hospital) and a prospective cohort (n = 156, 2014-2018, Tampere University Hospital). Preoperative symptoms were divided into primary and leading symptoms. Results were validated with the newer WHO 2021 classification criteria. Results The most common primary symptoms were epileptic seizure (30.8% retrospective, 28.2% prospective), cognitive disorder (13.2% retrospective, 16.0% prospective), headache (8.6% retrospective, 12.8% prospective), and motor paresis (7.0% retrospective, 7.1% prospective). Symptoms that predicted better survival were epileptic seizure and visual or other sense-affecting symptom in the retrospective cohort and epileptic seizure and headache in the prospective cohort. Predictors of poor survival were cognitive disorder, motor dysfunction, sensory symptom, tumor hemorrhage, speech disorder and dizziness in the retrospective cohort and cognitive disorder, motor dysfunction, sensory symptom, and dizziness in the prospective cohort. Motor dysfunction served as an independent predictor of survival in a multivariate model (OR = 1.636). Conclusion Primary and leading symptoms in diffuse gliomas are associated with prognoses in retrospective and prospective settings. Motor paresis was an independent prognostic factor for poor survival in multivariate analysis for grade 2-4 diffuse gliomas, especially in glioblastomas.
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Affiliation(s)
- Tomi Kivioja
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
| | - Jussi P. Posti
- Neurocenter, Department of Neurosurgery and Turku Brain Injury Center, Turku University Hospital and University of Turku, Turku, Finland
| | - Jussi Sipilä
- Department of Neurology, Siun Sote, North Karelia Central Hospital, Joensuu, Finland
- Clinical Neurosciences, University of Turku, Turku, Finland
| | - Minna Rauhala
- Faculty of Medicine and Health Technology, University of Tampere, Tampere, Finland
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
| | - Janek Frantzén
- Department of Neurosurgery, Turku University Hospital and University of Turku, Turku, Finland
| | - Maria Gardberg
- Turku University Hospital, Tyks Laboratories, Pathology and Institute of Biomedicine, University of Turku, Turku, Finland
| | - Melissa Rahi
- Department of Neurosurgery, Turku University Hospital and University of Turku, Turku, Finland
| | - Kirsi Rautajoki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Ville Vuorinen
- Department of Neurosurgery, Turku University Hospital and University of Turku, Turku, Finland
| | | | - Hannu Haapasalo
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Joonas Haapasalo
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
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5
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Lin J, Moradi E, Salenius K, Lehtipuro S, Häkkinen T, Laiho JE, Oikarinen S, Randelin S, Parikh HM, Krischer JP, Toppari J, Lernmark Å, Petrosino JF, Ajami NJ, She JX, Hagopian WA, Rewers MJ, Lloyd RE, Rautajoki KJ, Hyöty H, Nykter M. Distinct transcriptomic profiles in children prior to the appearance of type 1 diabetes-linked islet autoantibodies and following enterovirus infection. Nat Commun 2023; 14:7630. [PMID: 37993433 PMCID: PMC10665402 DOI: 10.1038/s41467-023-42763-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2023] [Accepted: 10/17/2023] [Indexed: 11/24/2023] Open
Abstract
Although the genetic basis and pathogenesis of type 1 diabetes have been studied extensively, how host responses to environmental factors might contribute to autoantibody development remains largely unknown. Here, we use longitudinal blood transcriptome sequencing data to characterize host responses in children within 12 months prior to the appearance of type 1 diabetes-linked islet autoantibodies, as well as matched control children. We report that children who present with insulin-specific autoantibodies first have distinct transcriptional profiles from those who develop GADA autoantibodies first. In particular, gene dosage-driven expression of GSTM1 is associated with GADA autoantibody positivity. Moreover, compared with controls, we observe increased monocyte and decreased B cell proportions 9-12 months prior to autoantibody positivity, especially in children who developed antibodies against insulin first. Lastly, we show that control children present transcriptional signatures consistent with robust immune responses to enterovirus infection, whereas children who later developed islet autoimmunity do not. These findings highlight distinct immune-related transcriptomic differences between case and control children prior to case progression to islet autoimmunity and uncover deficient antiviral response in children who later develop islet autoimmunity.
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Grants
- U01 DK063821 NIDDK NIH HHS
- UC4 DK063863 NIDDK NIH HHS
- UL1 TR002535 NCATS NIH HHS
- HHSN267200700014C NIDDK NIH HHS
- U01 DK128847 NIDDK NIH HHS
- U01 DK063790 NIDDK NIH HHS
- UL1 TR000064 NCATS NIH HHS
- U01 DK063836 NIDDK NIH HHS
- U01 DK063829 NIDDK NIH HHS
- U01 DK063865 NIDDK NIH HHS
- UC4 DK095300 NIDDK NIH HHS
- UC4 DK063861 NIDDK NIH HHS
- UC4 DK063829 NIDDK NIH HHS
- UC4 DK063821 NIDDK NIH HHS
- UC4 DK117483 NIDDK NIH HHS
- UC4 DK063836 NIDDK NIH HHS
- UC4 DK112243 NIDDK NIH HHS
- U01 DK124166 NIDDK NIH HHS
- U01 DK063861 NIDDK NIH HHS
- UC4 DK063865 NIDDK NIH HHS
- U01 DK063863 NIDDK NIH HHS
- UC4 DK106955 NIDDK NIH HHS
- UC4 DK100238 NIDDK NIH HHS
- Academy of Finland (Suomen Akatemia)
- Sigrid Juséliuksen Säätiö (Sigrid Jusélius Foundation)
- U.S. Department of Health & Human Services | NIH | National Institute of Diabetes and Digestive and Kidney Diseases (National Institute of Diabetes & Digestive & Kidney Diseases)
- EC | Horizon 2020 Framework Programme (EU Framework Programme for Research and Innovation H2020)
- The TEDDY Study is funded by U01 DK63829, U01 DK63861, U01 DK63821, U01 DK63865, U01 DK63863, U01 DK63836, U01 DK63790, UC4 DK63829, UC4 DK63861, UC4 DK63821, UC4 DK63865, UC4 DK63863, UC4 DK63836, UC4 DK95300, UC4 DK100238, UC4 DK106955, UC4 DK112243, UC4 DK117483, U01 DK124166, U01 DK128847, and Contract No. HHSN267200700014C from the National Institute of Diabetes and Digestive and Kidney Diseases (NIDDK), National Institute of Allergy and Infectious Diseases (NIAID), Eunice Kennedy Shriver National Institute of Child Health and Human Development (NICHD), National Institute of Environmental Health Sciences (NIEHS), Centers for Disease Control and Prevention (CDC), and JDRF. This work is supported in part by the NIH/NCATS Clinical and Translational Science Awards to the University of Florida (UL1 TR000064) and the University of Colorado (UL1 TR002535).
- Päivikki and Sakari Sohlberg's Foundation
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Affiliation(s)
- Jake Lin
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Biostatistics, Health Sciences, Faculty of Social Sciences, Tampere University, Tampere, Finland
- Finnish Institute of Molecular Medicine, FIMM, University of Helsinki, 00290, Helsinki, Finland
- Department of Medical Epidemiology and Biostatistics, Karolinska Institute, Stockholm, Sweden
| | - Elaheh Moradi
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland, Kuopio, 70150, Finland
| | - Karoliina Salenius
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Suvi Lehtipuro
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Tomi Häkkinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Jutta E Laiho
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sami Oikarinen
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Sofia Randelin
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Hemang M Parikh
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jeffrey P Krischer
- Health Informatics Institute, Morsani College of Medicine, University of South Florida, Tampa, FL, USA
| | - Jorma Toppari
- Research Centre for Integrative Physiology and Pharmacology, Institute of Biomedicine, and Centre for Population Health Research, University of Turku, Turku, Finland
- Department of Pediatrics, Turku University Hospital, Turku, Finland
| | - Åke Lernmark
- Department of Clinical Sciences, Lund University CRC, Skåne University Hospital, Malmö, Sweden
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Nadim J Ajami
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
- Platform for Innovative Microbiome & Translational Research (PRIME-TR), Moon Shots™ Program, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - Jin-Xiong She
- Jinfiniti Precision Medicine, Inc., Augusta, GA, USA
| | - William A Hagopian
- Pacific Northwest Research Institute, Seattle, WA, USA
- Department of Medicine, University of Washington, Seattle, WA, USA
| | - Marian J Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado, Aurora, CO, USA
| | - Richard E Lloyd
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, TX, USA
| | - Kirsi J Rautajoki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland.
| | - Heikki Hyöty
- Department of Virology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Fimlab Laboratories, Tampere, Finland.
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland.
- Foundation for the Finnish Cancer Institute, Helsinki, Finland.
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6
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Rautajoki KJ, Jaatinen S, Hartewig A, Tiihonen AM, Annala M, Salonen I, Valkonen M, Simola V, Vuorinen EM, Kivinen A, Rauhala MJ, Nurminen R, Maass KK, Lahtela SL, Jukkola A, Yli-Harja O, Helén P, Pajtler KW, Ruusuvuori P, Haapasalo J, Zhang W, Haapasalo H, Nykter M. Genomic characterization of IDH-mutant astrocytoma progression to grade 4 in the treatment setting. Acta Neuropathol Commun 2023; 11:176. [PMID: 37932833 PMCID: PMC10629206 DOI: 10.1186/s40478-023-01669-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 10/17/2023] [Indexed: 11/08/2023] Open
Abstract
As the progression of low-grade diffuse astrocytomas into grade 4 tumors significantly impacts patient prognosis, a better understanding of this process is of paramount importance for improved patient care. In this project, we analyzed matched IDH-mutant astrocytomas before and after progression to grade 4 from six patients (discovery cohort) with genome-wide sequencing, 21 additional patients with targeted sequencing, and 33 patients from Glioma Longitudinal AnalySiS cohort for validation. The Cancer Genome Atlas data from 595 diffuse gliomas provided supportive information. All patients in our discovery cohort received radiation, all but one underwent chemotherapy, and no patient received temozolomide (TMZ) before progression to grade 4 disease. One case in the discovery cohort exhibited a hypermutation signature associated with the inactivation of the MSH2 and DNMT3A genes. In other patients, the number of chromosomal rearrangements and deletions increased in grade 4 tumors. The cell cycle checkpoint gene CDKN2A, or less frequently RB1, was most commonly inactivated after receiving both chemo- and radiotherapy when compared to other treatment groups. Concomitant activating PDGFRA/MET alterations were detected in tumors that acquired a homozygous CDKN2A deletion. NRG3 gene was significantly downregulated and recurrently altered in progressed tumors. Its decreased expression was associated with poorer overall survival in both univariate and multivariate analysis. We also detected progression-related alterations in RAD51B and other DNA repair pathway genes associated with the promotion of error-prone DNA repair, potentially facilitating tumor progression. In our retrospective analysis of patient treatment and survival timelines (n = 75), the combination of postoperative radiation and chemotherapy (mainly TMZ) outperformed radiation, especially in the grade 3 tumor cohort, in which it was typically given after primary surgery. Our results provide further insight into the contribution of treatment and genetic alterations in cell cycle, growth factor signaling, and DNA repair-related genes to tumor evolution and progression.
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Affiliation(s)
- Kirsi J Rautajoki
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland.
- Tampere Institute for Advanced Study, Tampere University, Tampere, Finland.
| | - Serafiina Jaatinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Anja Hartewig
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Aliisa M Tiihonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Iida Salonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Masi Valkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Vili Simola
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Elisa M Vuorinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Anni Kivinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Minna J Rauhala
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Riikka Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Kendra K Maass
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro Oncology, German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Sirpa-Liisa Lahtela
- Department of Oncology, Tampere University Hospital and Tays Cancer Centre, Tampere, Finland
| | - Arja Jukkola
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Department of Oncology, Tampere University Hospital and Tays Cancer Centre, Tampere, Finland
| | - Olli Yli-Harja
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Institute for Systems Biology, Seattle, WA, USA
| | - Pauli Helén
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Kristian W Pajtler
- Hopp Children's Cancer Center Heidelberg (KiTZ), Heidelberg, Germany
- Division of Pediatric Neuro Oncology, German Cancer Research Center, German Cancer Consortium (DKTK), Heidelberg, Germany
- Department of Pediatric Oncology, Hematology, Immunology and Pulmonology, Heidelberg University Hospital, Heidelberg, Germany
| | - Pekka Ruusuvuori
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Joonas Haapasalo
- Department of Neurosurgery, Tampere University Hospital and Tampere University, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, USA
| | - Hannu Haapasalo
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Fimlab Laboratories Ltd., Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
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7
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Kaljunen H, Taavitsainen S, Kaarijärvi R, Takala E, Paakinaho V, Nykter M, Bova GS, Ketola K. Fanconi anemia pathway regulation by FANCI in prostate cancer. Front Oncol 2023; 13:1260826. [PMID: 38023254 PMCID: PMC10643534 DOI: 10.3389/fonc.2023.1260826] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2023] [Accepted: 09/29/2023] [Indexed: 12/01/2023] Open
Abstract
Prostate cancer is one of the leading causes of death among men worldwide, and thus, research on the genetic factors enabling the formation of treatment-resistant cancer cells is crucial for improving patient outcomes. Here, we report a cell line-specific dependence on FANCI and related signaling pathways to counteract the effects of DNA-damaging chemotherapy in prostate cancer. Our results reveal that FANCI depletion results in significant downregulation of Fanconi anemia (FA) pathway members in prostate cancer cells, indicating that FANCI is an important regulator of the FA pathway. Furthermore, we found that FANCI silencing reduces proliferation in p53-expressing prostate cancer cells. This extends the evidence that inactivation of FANCI may convert cancer cells from a resistant state to an eradicable state under the stress of DNA-damaging chemotherapy. Our results also indicate that high expression of FA pathway genes correlates with poorer survival in prostate cancer patients. Moreover, genomic alterations of FA pathway members are prevalent in prostate adenocarcinoma patients; mutation and copy number information for the FA pathway genes in seven patient cohorts (N = 1,732 total tumor samples) reveals that 1,025 (59.2%) tumor samples have an alteration in at least one of the FA pathway genes, suggesting that genomic alteration of the pathway is a prominent feature in patients with the disease.
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Affiliation(s)
- Heidi Kaljunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Roosa Kaarijärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Eerika Takala
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Ville Paakinaho
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Kirsi Ketola
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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8
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Nurminen A, Jaatinen S, Taavitsainen S, Högnäs G, Lesluyes T, Ansari-Pour N, Tolonen T, Haase K, Koskenalho A, Kankainen M, Jasu J, Rauhala H, Kesäniemi J, Nikupaavola T, Kujala P, Rinta-Kiikka I, Riikonen J, Kaipia A, Murtola T, Tammela TL, Visakorpi T, Nykter M, Wedge DC, Van Loo P, Bova GS. Cancer origin tracing and timing in two high-risk prostate cancers using multisample whole genome analysis: prospects for personalized medicine. Genome Med 2023; 15:82. [PMID: 37828555 PMCID: PMC10571458 DOI: 10.1186/s13073-023-01242-y] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2023] [Accepted: 10/02/2023] [Indexed: 10/14/2023] Open
Abstract
BACKGROUND Prostate cancer (PrCa) genomic heterogeneity causes resistance to therapies such as androgen deprivation. Such heterogeneity can be deciphered in the context of evolutionary principles, but current clinical trials do not include evolution as an essential feature. Whether or not analysis of genomic data in an evolutionary context in primary prostate cancer can provide unique added value in the research and clinical domains remains an open question. METHODS We used novel processing techniques to obtain whole genome data together with 3D anatomic and histomorphologic analysis in two men (GP5 and GP12) with high-risk PrCa undergoing radical prostatectomy. A total of 22 whole genome-sequenced sites (16 primary cancer foci and 6 lymph node metastatic) were analyzed using evolutionary reconstruction tools and spatio-evolutionary models. Probability models were used to trace spatial and chronological origins of the primary tumor and metastases, chart their genetic drivers, and distinguish metastatic and non-metastatic subclones. RESULTS In patient GP5, CDK12 inactivation was among the first mutations, leading to a PrCa tandem duplicator phenotype and initiating the cancer around age 50, followed by rapid cancer evolution after age 57, and metastasis around age 59, 5 years prior to prostatectomy. In patient GP12, accelerated cancer progression was detected after age 54, and metastasis occurred around age 56, 3 years prior to prostatectomy. Multiple metastasis-originating events were identified in each patient and tracked anatomically. Metastasis from prostate to lymph nodes occurred strictly ipsilaterally in all 12 detected events. In this pilot, metastatic subclone content analysis appears to substantially enhance the identification of key drivers. Evolutionary analysis' potential impact on therapy selection appears positive in these pilot cases. CONCLUSIONS PrCa evolutionary analysis allows tracking of anatomic site of origin, timing of cancer origin and spread, and distinction of metastatic-capable from non-metastatic subclones. This enables better identification of actionable targets for therapy. If extended to larger cohorts, it appears likely that similar analyses could add substantial biological insight and clinically relevant value.
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Affiliation(s)
- Anssi Nurminen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Serafiina Jaatinen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Gunilla Högnäs
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Tom Lesluyes
- The Francis Crick Institute, London, NW1 1AT, UK
| | - Naser Ansari-Pour
- MRC Molecular Haematology Unit, Weatherall Institute of Molecular Medicine, University of Oxford, Oxford, UK
| | - Teemu Tolonen
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Kerstin Haase
- The Francis Crick Institute, London, NW1 1AT, UK
- Charité - Universitätsmedizin Berlin, corporate member of Freie Universität Berlin and Humboldt Universität Zu Berlin, ECRC Experimental and Clinical Research Center, Berlin, Germany
| | - Antti Koskenalho
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Matti Kankainen
- Institute for Molecular Medicine Finland, University of Helsinki, Tukholmankatu 8, Helsinki, 00290, Finland
| | - Juho Jasu
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Hanna Rauhala
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Jenni Kesäniemi
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Tiia Nikupaavola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - Paula Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Irina Rinta-Kiikka
- Imaging Centre, Department of Radiology, Tampere University Hospital, Tampere, Finland
| | - Jarno Riikonen
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Antti Kaipia
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teemu Murtola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teuvo L Tammela
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Department of Urology, TAYS Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland
| | - David C Wedge
- Manchester Cancer Research Centre, Division of Cancer Sciences, University of Manchester, Manchester, M20 4GJ, UK
| | - Peter Van Loo
- The Francis Crick Institute, London, NW1 1AT, UK
- Department of Genetics, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
- Department of Genomic Medicine, The University of Texas MD Anderson Cancer Center, Houston, TX, 77030, USA
| | - G Steven Bova
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, PO Box 100, 33014, Tampere, Finland.
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9
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Sattari M, Kohvakka A, Moradi E, Rauhala H, Urhonen H, Isaacs WB, Nykter M, Murtola TJ, Tammela TLJ, Latonen L, Bova GS, Kesseli J, Visakorpi T. Identification of long noncoding RNAs with aberrant expression in prostate cancer metastases. Endocr Relat Cancer 2023:ERC-22-0247. [PMID: 37140987 DOI: 10.1530/erc-22-0247] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 08/23/2022] [Accepted: 05/03/2023] [Indexed: 05/05/2023]
Abstract
Prostate cancer (PCa) is the second-most common cause of male cancer-related death in western industrialized countries, and the emergence of metastases is a key challenge in the treatment of PCa. Accumulating studies have shown that long noncoding RNAs (lncRNAs) play an important role in the regulation of diverse cellular and molecular processes during the development and progression of cancer. Here, we utilized a unique cohort of castration-resistant prostate cancer metastases (mCRPC) and corresponding localized tumors and RNA sequencing (RNA-seq). First, we showed that patient-to-patient variability accounted for most of the variance in lncRNA expression between the samples, suggesting that genomic alterations in the samples are the main drivers of lncRNA expression in PCa metastasis. Subsequently, we identified 27 lncRNAs with differential expression (DE-lncRNAs) between metastases and corresponding primary tumors, suggesting that they are mCRPC-specific lncRNAs. Analyses of potential regulation by transcription factors (TFs) revealed that approximately half of the DE-lncRNAs have at least one binding site for the androgen receptor (AR) in their regulatory regions. In addition, transcription factor enrichment analysis revealed the enrichment of binding sites for PCa-associated TFs, such as FOXA1 and HOXB13, in the regulatory regions of the DE-lncRNAs. In a cohort of prostatectomy-treated prostate tumors, four of the DE-lncRNAs showed association with progression-free time, and two of them (lnc-SCFD2-2, and lnc-R3HCC1L-8) were independent prognostic markers. Our study highlights several mCRPC-specific lncRNAs that might be important in the progression of the disease to the metastatic stage and may also serve as potential biomarkers for aggressive PCa.
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Affiliation(s)
- Mina Sattari
- M Sattari, faculty of medicine and health technology, Tampere University, Tampere, 33014, Finland
| | - Annika Kohvakka
- A Kohvakka, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Elaheh Moradi
- E Moradi, A.I. Virtanen Institute for Molecular Sciences, University of Eastern Finland - Kuopio Campus, Kuopio, Finland
| | - Hanna Rauhala
- H Rauhala, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Henna Urhonen
- H Urhonen, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - William B Isaacs
- W Isaacs, The James Buchanan Brady Urological Institute, Johns Hopkins, Baltimore, United States
| | - Matti Nykter
- M Nykter, Faculty of medicine and health technology, Tays Cancer Center, Tampere, Finland
| | - Teemu J Murtola
- T Murtola, Faculty of Medicine and Health Technology, Tampere Universities, Tampere, Finland
| | - Teuvo L J Tammela
- T Tammela, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Leena Latonen
- L Latonen, Institute of Biomedicine, University of Eastern Finland School of Medicine, Kuopio, Finland
| | - G Steven Bova
- G Bova, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Juha Kesseli
- J Kesseli, Faculty of medicine and health technology, Tampere University, Tampere, Finland
| | - Tapio Visakorpi
- T Visakorpi, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
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10
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Aakula A, Sharma M, Tabaro F, Nätkin R, Kamila J, Honkanen H, Schapira M, Arrowsmith C, Nykter M, Westermarck J. RAS and PP2A activities converge on epigenetic gene regulation. Life Sci Alliance 2023; 6:e202301928. [PMID: 36858798 PMCID: PMC9979842 DOI: 10.26508/lsa.202301928] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2023] [Revised: 02/12/2023] [Accepted: 02/13/2023] [Indexed: 03/03/2023] Open
Abstract
RAS-mediated human cell transformation requires inhibition of the tumor suppressor protein phosphatase 2A (PP2A). However, the phosphoprotein targets and cellular processes in which RAS and PP2A activities converge in human cancers have not been systematically analyzed. Here, we discover that phosphosites co-regulated by RAS and PP2A are enriched on proteins involved in epigenetic gene regulation. As examples, RAS and PP2A co-regulate the same phosphorylation sites on HDAC1/2, KDM1A, MTA1/2, RNF168, and TP53BP1. We validate RAS- and PP2A-elicited regulation of HDAC1/2 chromatin recruitment, of RNF168-TP53BP1 interaction, and of gene expression. Consistent with their known synergistic effects in cancer, RAS activation and PP2A inhibition resulted in epigenetic reporter derepression and activation of oncogenic transcription. Transcriptional derepression by PP2A inhibition was associated with an increase in euchromatin and a decrease in global DNA methylation. Collectively, the results indicate that epigenetic protein complexes constitute a significant point of convergence for RAS hyperactivity and PP2A inhibition in cancer. Furthermore, the work provides an important resource for future studies focusing on phosphoregulation of epigenetic gene regulation in cancer and in other RAS/PP2A-regulated cellular processes.
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Affiliation(s)
- Anna Aakula
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Mukund Sharma
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Francesco Tabaro
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Reetta Nätkin
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Jesse Kamila
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Henrik Honkanen
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
| | - Matthieu Schapira
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
- Department of Pharmacology and Toxicology, University of Toronto, Toronto, Canada
| | - Cheryl Arrowsmith
- Structural Genomics Consortium, University of Toronto, Toronto, Canada
- Princess Margaret Cancer Centre, University Health Network, Toronto, Canada
- Department of Medical Biophysics, University of Toronto, Toronto, Canada
| | - Matti Nykter
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Jukka Westermarck
- Turku Bioscience Centre, University of Turku and Åbo Akademi University, Turku, Finland
- Institute of Biomedicine, University of Turku, Turku, Finland
- InFLAMES Research Flagship Center, University of Turku, Turku, Finland
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11
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Hamis S, Somervuo P, Ågren JA, Tadele DS, Kesseli J, Scott JG, Nykter M, Gerlee P, Finkelshtein D, Ovaskainen O. Spatial cumulant models enable spatially informed treatment strategies and analysis of local interactions in cancer systems. J Math Biol 2023; 86:68. [PMID: 37017776 PMCID: PMC10076412 DOI: 10.1007/s00285-023-01903-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2022] [Revised: 01/13/2023] [Accepted: 03/09/2023] [Indexed: 04/06/2023]
Abstract
Theoretical and applied cancer studies that use individual-based models (IBMs) have been limited by the lack of a mathematical formulation that enables rigorous analysis of these models. However, spatial cumulant models (SCMs), which have arisen from theoretical ecology, describe population dynamics generated by a specific family of IBMs, namely spatio-temporal point processes (STPPs). SCMs are spatially resolved population models formulated by a system of differential equations that approximate the dynamics of two STPP-generated summary statistics: first-order spatial cumulants (densities), and second-order spatial cumulants (spatial covariances). We exemplify how SCMs can be used in mathematical oncology by modelling theoretical cancer cell populations comprising interacting growth factor-producing and non-producing cells. To formulate model equations, we use computational tools that enable the generation of STPPs, SCMs and mean-field population models (MFPMs) from user-defined model descriptions (Cornell et al. Nat Commun 10:4716, 2019). To calculate and compare STPP, SCM and MFPM-generated summary statistics, we develop an application-agnostic computational pipeline. Our results demonstrate that SCMs can capture STPP-generated population density dynamics, even when MFPMs fail to do so. From both MFPM and SCM equations, we derive treatment-induced death rates required to achieve non-growing cell populations. When testing these treatment strategies in STPP-generated cell populations, our results demonstrate that SCM-informed strategies outperform MFPM-informed strategies in terms of inhibiting population growths. We thus demonstrate that SCMs provide a new framework in which to study cell-cell interactions, and can be used to describe and perturb STPP-generated cell population dynamics. We, therefore, argue that SCMs can be used to increase IBMs' applicability in cancer research.
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Affiliation(s)
- Sara Hamis
- Tampere Institute for Advanced Study, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland.
| | - Panu Somervuo
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
| | - J Arvid Ågren
- Department of Evolutionary Biology, Uppsala University, Uppsala, Sweden
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
| | - Dagim Shiferaw Tadele
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
- Department for Medical Genetics, Oslo University Hospital, Ullevål, Oslo, Norway
| | - Juha Kesseli
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Jacob G Scott
- Department of Translational Hematology and Oncology Research, Cleveland Clinic, Cleveland, OH, USA
- Case Western Reserve School of Medicine, Cleveland, OH, USA
- Department of Radiation Oncology, Cleveland Clinic, Cleveland, OH, USA
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Philip Gerlee
- Mathematical Sciences, Chalmers University of Technology, Gothenburg, Sweden
- Mathematical Sciences, University of Gothenburg, Gothenburg, Sweden
| | - Dmitri Finkelshtein
- Department of Mathematics, Faculty of Science and Engineering, Swansea University, Swansea, UK
| | - Otso Ovaskainen
- Department of Biological and Environmental Science, University of Jyväskylä, Jyväskylä, Finland
- Organismal and Evolutionary Biology Research Programme, Faculty of Biological and Environmental Sciences, University of Helsinki, Helsinki, Finland
- Department of Biology, Centre for Biodiversity Dynamics, Norwegian University of Science and Technology, Trondheim, Norway
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12
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Kiviaho A, Kallio HM, Eerola SK, Vuorinen EM, Häkkinen T, Taavitsainen S, Afyounian E, Tolonen T, Kesseli J, Urbanucci A, Rautajoki KJ, Tammela TL, Visakorpi T, Nykter M. Abstract 5644: Spatially resolved transcriptomics points to distinct malignant cell populations within primary and castration resistant prostate cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-5644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
Background: Prostate cancer (PCa) is the second most common cancer in men. Despite its high prevalence, many patients carry an indolent form of the disease and are thus suspect to overtreatment. Conversely, some cases treated with androgen deprivation therapy can develop into castration resistant prostate cancer (CRPC), for which there is no curative treatment. Understanding why some tumors are more aggressive than others could lead to more accurate patient risk stratification. Here we characterize cancer and normal cell subpopulations within prostate tissue in their spatial context using a multimodal integrative approach.
Methods: We performed spatially resolved transcriptomics (ST) on a set of primary tumor PCa, CRPC and benign prostatic hyperplasia (BPH) patient samples. In addition to ST, we produced RNA-seq, DNA-seq and assay for transposase accessible chromatin using sequencing (ATAC-seq) data, allowing for multiomic integration within and across sample categories. We performed extensive analysis of ST data, employing unsupervised clustering, spot expression signal deconvolution, differential gene expression analysis and copy number variation (CNV) inference.
Main Results: The systematic analysis of spot expression profiles revealed a high degree of variation in nearby tissue regions, as we found up to three unique luminal cell populations inside a one millimeter radius in PCa. Similarly in locally recurrent CRPC, we identified cumulative CNVs in proximal luminal cell populations, with the inferred CNV profiles validated through DNA-seq. A set of marker genes was calculated for each unique cell population, with multiple PCa associated genes found to be differentially expressed. Although we observed significant variation in the luminal cell populations, the stromal gene expression was markedly similar across all samples.
Conclusions: We discovered shared, similar and unique cell populations both within and across different PCa and CRPC sections. We observed various luminal cell populations with distinct gene expression profiles in samples from both progression stages. The close spatial proximity of these cell clusters suggests that ST can be used to discover and examine finely detailed populations in their original spatial environment.
Citation Format: Antti Kiviaho, Heini M. Kallio, Sini K. Eerola, Elisa M. Vuorinen, Tomi Häkkinen, Sinja Taavitsainen, Ebrahim Afyounian, Teemu Tolonen, Juha Kesseli, Alfonso Urbanucci, Kirsi J. Rautajoki, Teuvo L. Tammela, Tapio Visakorpi, Matti Nykter. Spatially resolved transcriptomics points to distinct malignant cell populations within primary and castration resistant prostate cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 5644.
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Affiliation(s)
- Antti Kiviaho
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Heini M. Kallio
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Sini K. Eerola
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Elisa M. Vuorinen
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Tomi Häkkinen
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Sinja Taavitsainen
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Ebrahim Afyounian
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Teemu Tolonen
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Juha Kesseli
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Alfonso Urbanucci
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Kirsi J. Rautajoki
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Teuvo L. Tammela
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Tapio Visakorpi
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
| | - Matti Nykter
- 1Tampere University, Faculty of Medicine and Health Technology, Tampere, Finland
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13
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Ojanen MJT, Caro FM, Aittomäki S, Ploquin MJ, Ortutay Z, Pekkarinen M, Kesseli J, Vähätupa M, Määttä J, Nykter M, Junttila IS, Järvinen TAH, O Shea JJ, Biron CA, Pesu M. FURIN regulates cytotoxic T lymphocyte effector function and memory cell transition in mice. Eur J Immunol 2023:e2250246. [PMID: 37015057 DOI: 10.1002/eji.202250246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2022] [Revised: 03/16/2023] [Accepted: 04/03/2023] [Indexed: 04/06/2023]
Abstract
The proprotein convertase subtilisin/kexins (PCSKs) regulate biological actions by cleaving immature substrate proteins. The archetype PCSK, FURIN, promotes the pathogenicity of viruses by proteolytically processing viral proteins. FURIN has also important regulatory functions in both innate and adaptive immune responses but its role in the CD8+ CTLs remains enigmatic. We used a T cell specific FURIN deletion in vivo to demonstrate that FURIN promotes host response against the CTL-dependent lymphocytic choriomeningitis virus by virtue of restricting viral burden and augmenting IFNG production. We also characterized Furin KO CD8+ T cells ex vivo, including after their activation with FURIN regulating cytokines IL12 or TGFB1. Furin KO CD8+ T cells show an inherently activated phenotype characterized by the up-regulation of effector genes and increased frequencies of CD44+, TNF+ and IFNG+ cells. In the activated CTLs FURIN regulates the productions of IL2, TNF and GZMB and the genes associated with the TGFBR-signaling pathway. FURIN also controls the expression of Eomes, Foxo1 and Bcl6 and the levels of ITGAE and CD62L, which implies a role in the development of CTL memory. Collectively, our data suggest that the T cell expressed FURIN is important for host responses in viral infections, CTL homeostasis/activation and memory development. This article is protected by copyright. All rights reserved.
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Affiliation(s)
- Markus J T Ojanen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Fernanda Munoz Caro
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Saara Aittomäki
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Mickaël J Ploquin
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, and The Warren Alpert Medical School, Brown University, Providence, RI, 02912, USA
| | - Zsuzsanna Ortutay
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Meeri Pekkarinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Maria Vähätupa
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Juuso Määttä
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
| | - Ilkka S Junttila
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
- Fimlab Laboratories Ltd, Tampere, FI-33520, Finland
- Faculty of Medicine, University of Oulu, Oulu, FI-90570, Finland
- Department of Clinical Microbiology, Nordlab, Oulu University Hospital, Oulu, FI-90120, Finland
| | - Tero A H Järvinen
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
- Tampere University Hospital, Tampere, FI-33520, Finland
| | - John J O Shea
- Lymphocyte Cell Biology Section, Molecular Immunology and Inflammation Branch, National Institute of Arthritis and Musculoskeletal and Skin Diseases, National Institutes of Health, Bethesda, MD, 20892, USA
| | - Christine A Biron
- Department of Molecular Microbiology and Immunology, Division of Biology and Medicine, and The Warren Alpert Medical School, Brown University, Providence, RI, 02912, USA
| | - Marko Pesu
- Faculty of Medicine and Health Technology, Tampere University, Tampere, FI-33014, Finland
- Fimlab Laboratories Ltd, Tampere, FI-33520, Finland
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14
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Sharma M, Aakula A, Tabaro F, Honkanen H, Kamila J, Schapira M, Arrowsmith C, Nykter M, Westermarck JK. Abstract 4727: RAS and PP2A activities converge on phosphoregulation of epigenetic complexes in cancer. Cancer Res 2023. [DOI: 10.1158/1538-7445.am2023-4727] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/07/2023]
Abstract
Abstract
RAS-mediated human cell transformation requires inhibition of the tumor suppressor Protein Phosphatase 2A (PP2A). Both RAS and PP2A mediate their effects by phosphoregulation, but phosphoprotein targets in which RAS and PP2A activities converge in human cancers have not been systematically analyzed. Here, based on mass spectrometry phosphoproteome data, we discover that phosphosites co-regulated by RAS and PP2A are enriched on proteins involved in epigenetic gene regulation. As examples, RAS and PP2A co-regulate the same phosphorylation sites on HDAC1/2, KDM1A, MTA1/2, RNF168 and TP53BP1. Mechanistically, we validate co-regulation of NuRD chromatin repressor complex by RAS and PP2A. Consistent with their known synergistic effects in cancer, RAS activation and PP2A inhibition resulted in epigenetic reporter de-repression and activation of oncogenic transcription. Notably, transcriptional de-repression by PP2A inhibition was associated with increased euchromatin and decrease in global DNA methylation. In RAS-driven cancers, PP2A activity is inhibited by nuclear PP2A inhibitor proteins PME-1 and SET. We further demonstrate that these PP2A inhibitors drive oncogenic transcription, but that their transcriptional targets are highly diversified. Whereas PME-1 controls RAS and MYC-driven transcription, SET controls TP53 targets and G2/M checkpoint genes. We further provide evidence that these nuclear PP2A inhibitors significantly differ in their roles in regulating DNA methylation. Collectively the results indicate that epigenetic protein complexes involved in oncogenic gene expression constitute a significant point of convergence for RAS hyperactivity and PP2A inhibition in cancer. Further, the results provide a rich source for future understanding of phosphorylation as a previously unappreciated layer of regulation of epigenetic gene regulation in cancer, and in other RAS/PP2A-regulated cellular processes.
Citation Format: Mukund Sharma, Anna Aakula, Francesco Tabaro, Henrik Honkanen, Jesse Kamila, Matthieu Schapira, Cheryl Arrowsmith, Matti Nykter, Jukka K. Westermarck. RAS and PP2A activities converge on phosphoregulation of epigenetic complexes in cancer. [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2023; Part 1 (Regular and Invited Abstracts); 2023 Apr 14-19; Orlando, FL. Philadelphia (PA): AACR; Cancer Res 2023;83(7_Suppl):Abstract nr 4727.
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15
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Severson TM, Zhu Y, Prekovic S, Schuurman K, Nguyen HM, Brown LG, Hakkola S, Kim Y, Kneppers J, Linder S, Stelloo S, Lieftink C, van der Heijden M, Nykter M, van der Noort V, Sanders J, Morris B, Jenster G, van Leenders GJLH, Pomerantz M, Freedman ML, Beijersbergen RL, Urbanucci A, Wessels L, Corey E, Zwart W, Bergman AM. Enhancer profiling identifies epigenetic markers of endocrine resistance and reveals therapeutic options for metastatic castration-resistant prostate cancer patients. medRxiv 2023:2023.02.24.23286403. [PMID: 36865297 PMCID: PMC9980263 DOI: 10.1101/2023.02.24.23286403] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/01/2023]
Abstract
Androgen Receptor (AR) signaling inhibitors, including enzalutamide, are treatment options for patients with metastatic castration-resistant prostate cancer (mCRPC), but resistance inevitably develops. Using metastatic samples from a prospective phase II clinical trial, we epigenetically profiled enhancer/promoter activities with H3K27ac chromatin immunoprecipitation followed by sequencing, before and after AR-targeted therapy. We identified a distinct subset of H3K27ac-differentially marked regions that associated with treatment responsiveness. These data were successfully validated in mCRPC patient-derived xenograft models (PDX). In silico analyses revealed HDAC3 as a critical factor that can drive resistance to hormonal interventions, which we validated in vitro . Using cell lines and mCRPC PDX tumors in vitro , we identified drug-drug synergy between enzalutamide and the pan-HDAC inhibitor vorinostat, providing therapeutic proof-of-concept. These findings demonstrate rationale for new therapeutic strategies using a combination of AR and HDAC inhibitors to improve patient outcome in advanced stages of mCRPC.
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16
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Alanen E, Heikkinen S, Nurminen R, Nykter M, Haapasalo H, Hirvonen E, Pitkäniemi J, Rautajoki KJ. Early-onset grade 2-3 diffuse gliomas and schwannomas increase the risk of central nervous system tumors among the patients' relatives. Neurooncol Adv 2023; 5:vdad008. [PMID: 36950216 PMCID: PMC10025807 DOI: 10.1093/noajnl/vdad008] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Background Central nervous system (CNS) tumors are a heterogeneous group of tumors that include several aggressive malignancies with a high mortality rate. This study aimed to evaluate the familial relative risk of CNS tumors in family members of early-onset index cases (probands) in and between diffuse glioma, non-diffuse glioma, meningioma, and other CNS tumors. Methods We retrieved tumor data from the Finnish cancer registry and familial relationships data from the population information system. We ascertained 5408 probands diagnosed with primary CNS tumors (age ≤40 years) between 1970 and 2012 in Finland. We report the standardized incidence ratios as a measure of familial aggregation using Poisson regression. Results The risk of early-onset diffuse glioma increased among siblings of probands with the same tumor [SIR 3.85, 95% confidence interval (CI): 1.66-7.59], with association mainly returning to grade 2-3 diffuse gliomas. Early-onset other CNS tumors were associated with an increased risk of other CNS tumors, early-onset meningioma, and late-onset diffuse glioma in 1st-degree relatives. The elevated risk of other CNS tumors was largely caused by schwannomas (SIR 59.44, 95% CI: 27.18-112.84 for 1st-degree relatives) and associated with neurofibromatosis. No tumor syndrome was associated with an increased risk of diffuse gliomas. Conclusions The early onset of grade 2-3 diffuse gliomas is associated with an increased risk of similar tumor entities. Early-onset schwannomas dramatically increase CNS tumor risk with a broader tumor-type profile. In future studies, it would be important to identify the underlying shared hereditary factors that contribute to the development of familial diffuse gliomas.
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Affiliation(s)
| | | | - Riikka Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Hannu Haapasalo
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Fimlab Laboratories ltd., Tampere University Hospital, Tampere, Finland
| | - Elli Hirvonen
- Finnish Cancer Registry, Cancer Society of Finland, Helsinki, Finland
| | - Janne Pitkäniemi
- Janne Pitkäniemi, PhD, Finnish Cancer Registry, Unioninkatu 22, 00130, Helsinki, Finland ()
| | - Kirsi J Rautajoki
- Corresponding Authors: Kirsi J. Rautajoki, PhD, BioMediTech Unit, Faculty of Medicine and Health Technology, Tampere University, Arvo Ylpön katu 34, 33520 Tampere, Finland, ()
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17
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Nätkin R, Pennanen P, Syvälä H, Bläuer M, Kesseli J, Tammela TLJ, Nykter M, Murtola TJ. Adaptive and non-adaptive gene expression responses in prostate cancer during androgen deprivation. PLoS One 2023; 18:e0281645. [PMID: 36809527 PMCID: PMC9942993 DOI: 10.1371/journal.pone.0281645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2022] [Accepted: 01/30/2023] [Indexed: 02/23/2023] Open
Abstract
Androgen deprivation therapy is the cornerstone treatment of advanced prostate cancer. Eventually prostate cancer cells overcome androgen deprivation therapy, giving rise to castration resistant prostate cancer (CRPC) characterized by increased androgen receptor (AR) activity. Understanding the cellular mechanisms leading to CRPC is needed for development of novel treatments. We used long-term cell cultures to model CRPC; a testosterone-dependent cell line (VCaP-T) and cell line adapted to grow in low testosterone (VCaP-CT). These were used to uncover persistent and adaptive responses to testosterone level. RNA was sequenced to study AR-regulated genes. Expression level changed due to testosterone depletion in 418 genes in VCaP-T (AR-associated genes). To evaluate significance for CRPC growth, we compared which of them were adaptive i.e., restored expression level in VCaP-CT. Adaptive genes were enriched to steroid metabolism, immune response and lipid metabolism. The Cancer Genome Atlas Prostate Adenocarcinoma data were used to assess the association with cancer aggressiveness and progression-free survival. Expressions of 47 AR-associated or association gaining genes were statistically significant markers for progression-free survival. These included genes related to immune response, adhesion and transport. Taken together, we identified and clinically validated multiple genes being linked with progression of prostate cancer and propose several novel risk genes. Possible use as biomarkers or therapeutic targets should be studied further.
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Affiliation(s)
- Reetta Nätkin
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, Finland
- * E-mail: (RN); (TJM)
| | - Pasi Pennanen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Heimo Syvälä
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Merja Bläuer
- Tampere University Hospital and Faculty of Medicine and Health Technology, Tampere Pancreas Laboratory and Department of Gastroenterology and Alimentary Tract Surgery, Tampere University, Tampere, Finland
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Teuvo L. J. Tammela
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Urology, Tays Cancer Center, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Teemu J. Murtola
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Urology, Tays Cancer Center, Tampere, Finland
- * E-mail: (RN); (TJM)
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18
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Kukkonen K, Autio-Kimura B, Rauhala H, Kesseli J, Nykter M, Latonen L, Visakorpi T. Nonmalignant AR-positive prostate epithelial cells and cancer cells respond differently to androgen. Endocr Relat Cancer 2022; 29:717-733. [PMID: 36219867 PMCID: PMC9644224 DOI: 10.1530/erc-22-0108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/04/2022] [Accepted: 10/10/2022] [Indexed: 11/07/2022]
Abstract
Prostate cancer research suffers from the lack of suitable models to study the role of normal cells in prostate carcinogenesis. To address this challenge, we developed a cell line model mimicking luminal prostate epithelial cells by modifying the immortalized prostate epithelial cell line RWPE-1 to constitutively express the androgen receptor (AR). RWPE-1-AR cells express known AR target genes, and exhibit coexpression of luminal and basal markers characteristic of transient amplifying cells, and an RNA signature resembling prostate luminal progenitor cells. Under unstimulated conditions, constitutive AR expression does not have a biologically significant effect on the proliferation of RWPE-1 cells, but when stimulated by androgens, growth is retarded. The transcriptional response of RWPE-1-AR cells to androgen stimulation involves suppression of the growth-related KRAS pathway and is thus markedly different from that of the prostate cancer cell line LNCaP and its derivative AR-overexpressing LNCaP-ARhi cells, in which growth- and cancer-related pathways are upregulated. Hence, the nonmalignant AR-positive RWPE-1-AR cell line model could be used to study the transformation of the prostate epithelium.
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Affiliation(s)
- Konsta Kukkonen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Bryn Autio-Kimura
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Hanna Rauhala
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
| | - Leena Latonen
- Foundation for the Finnish Cancer Institute, Helsinki, Finland
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere University Hospital, Tampere, Finland
- Fimlab Laboratories Ltd, Tampere, Finland
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19
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Hartewig A, Granberg K, Jaatinen S, Tiihonen A, Annala M, Vuorinen E, Kivinen A, Rauhala M, Maass K, Pajtler K, Yli-Harja O, Helén P, Haapasalo J, Zhang W, Haapasalo H, Nykter M. EPCO-11. GATEKEEPER INACTIVATION DRIVES TUMOR PROGRESSION TO GRADE IV ASTROCYTOMA. Neuro Oncol 2022. [PMCID: PMC9660466 DOI: 10.1093/neuonc/noac209.446] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
IDH-mutant low-grade diffuse astrocytomas frequently progress to grade IV astrocytomas with implications for patient prognosis. To better understand this process, we applied whole-genome and transcriptome sequencing to matched tumor samples collected before and after progression to grade IV astrocytomas from five patients. All tumors carried an IDH1 mutation. The number of chromosomal rearrangements was increased between 1.3 and 3.5-fold in the tumors upon progression, with the exception of one case, in which the increase was only 1.03-fold. This case exhibited a hypermutation signature caused by homozygous deletion of the MSH2 gene, which encodes a member of the DNA mismatch repair complex. The most common genomic alterations acquired at progression were homozygous deletions in the CDKN2A/ RB1 -pathway or hemizygous deletion of PTEN. Additionally, PDGFRA was amplified in two grade IV tumors, with concordantly increased expression. For one of these cases, a PDGFRA-amplified subclone is likely to be present already in the low-grade astrocytoma. We further detected intrachromosomal rearrangements closeby the genes NRG3 in the progressed tumors as well as in the The Cancer Genome Atlas (TCGA) cohort. The expression of NRG3 decreased with increasing grade in the TCGA cohort and the gene was frequently deleted. Lower NRG3 expression was associated with shorter survival in the TCGA cohort. Several miRNAs showed differential expression upon progression. For two miRNAs the predicted targets were associated with cell cycle regulation and we detected inverse correlation between miRNA and target mRNA expression. While progression seems to occur via different pathways, the predicted outcome for many of the alterations was the inactivation of tumor suppressor genes and further dysregulation of cell proliferation.
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Affiliation(s)
- Anja Hartewig
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Kirsi Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Serafiina Jaatinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Aliisa Tiihonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Matti Annala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Elisa Vuorinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Anni Kivinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Minna Rauhala
- Department of Neurosurgery, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Kendra Maass
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany , Heidelberg , Germany
| | - Kristian Pajtler
- Hopp Children’s Cancer Center Heidelberg (KiTZ), Heidelberg, Germany , Heidelberg , Germany
| | - Olli Yli-Harja
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland , Tampere , Finland
| | - Pauli Helén
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland , Tampere , Finland
| | - Joonas Haapasalo
- Department of Neurosurgery, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States , Winston-Salem , USA
| | - Hannu Haapasalo
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
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20
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Pekkarinen M, Nordfors K, Uusi-Mäkelä J, Kytölä V, Rauhala M, Urhonen H, Häyrynen S, Afyounian E, Yli-Harja O, Zhang W, Helen P, Lohi O, Haapasalo H, Haapasalo J, Nykter M, Kesseli J, Granberg K. EPCO-34. INTEGRATIVE DNA METHYLATION ANALYSIS OF PEDIATRIC BRAIN TUMORS REVEALS TUMOR TYPE-SPECIFIC DEVELOPMENTAL TRAJECTORIES AND EPIGENETIC SIGNATURES OF MALIGNANCY. Neuro Oncol 2022. [DOI: 10.1093/neuonc/noac209.468] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Abstract
Understanding oncogenic epigenetic mechanisms in brain tumors is crucial for improved diagnosis and treatment. Recently DNA methylation has proven to be powerful for brain tumor characterization and diagnostic classification. To evaluate tumor type specific features, we compared atypical teratoid/rhabdoid tumors (AT/RTs), medulloblastomas (MBs), and choroid plexus tumors with each other by integrating DNA methylation (507 samples), gene expression (120 samples), and transcription factor (TF) -binding data. Different tumor entities were used to find unique changes affecting each of the entities and further to identify functions driven by these changes. Our results provide insight on how the aberrant DNA methylation induces oncogenesis of AT/RTs. These tumors are known for their aggressiveness and exceptionally low mutation rates. Our results suggest that in AT/RT, elevated DNA methylation masks the binding sites of TFs such as NEUROD1, ASCL1 and MYCN driving neural development. DNA methylation in AT/RTs is also associated with reduced gene expression for specific neural regulators such as NEUROG1 and NEUROD2. For MBs, DNA methylation patterns predict a more advanced differentiation state. In MB, we found masked TF binding sites for TFs such as REST and ZEB1 that normally inhibit neural differentiation. We then wanted to further characterize DNA methylation and compared these tumors to pluripotent stem cells (PSCs) and normal fetal brain samples. As a result, we were able to find two different regulatory programs in AT/RTs: One in which DNA methylation is similar to PSCs and which harbors mostly neural TF binding sites. Second program has AT/RT-specific DNA methylation, and these sites are uniquely associated with polycomb repressive complex 2 members. However, this second program also covers neural TF binding sites and is likely to have relevance in oncogenic regulation.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Olli Yli-Harja
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland , Tampere , Finland
| | - Wei Zhang
- Cancer Genomics and Precision Oncology, Wake Forest Baptist Comprehensive Cancer Center, Winston-Salem, NC, United States , Winston-Salem , USA
| | - Pauli Helen
- Tampere University Hospital , Tampere , Finland
| | - Olli Lohi
- Tampere University Hospital , Tampere , Finland
| | - Hannu Haapasalo
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Joonas Haapasalo
- Department of Neurosurgery, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
| | | | - Kirsi Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland , Tampere , Finland
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21
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Herberts C, Annala M, Sipola J, Ng SWS, Chen XE, Nurminen A, Korhonen OV, Munzur AD, Beja K, Schönlau E, Bernales CQ, Ritch E, Bacon JVW, Lack NA, Nykter M, Aggarwal R, Small EJ, Gleave ME, Quigley DA, Feng FY, Chi KN, Wyatt AW. Deep whole-genome ctDNA chronology of treatment-resistant prostate cancer. Nature 2022; 608:199-208. [PMID: 35859180 DOI: 10.1038/s41586-022-04975-9] [Citation(s) in RCA: 60] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2021] [Accepted: 06/14/2022] [Indexed: 01/20/2023]
Abstract
Circulating tumour DNA (ctDNA) in blood plasma is an emerging tool for clinical cancer genotyping and longitudinal disease monitoring1. However, owing to past emphasis on targeted and low-resolution profiling approaches, our understanding of the distinct populations that comprise bulk ctDNA is incomplete2-12. Here we perform deep whole-genome sequencing of serial plasma and synchronous metastases in patients with aggressive prostate cancer. We comprehensively assess all classes of genomic alterations and show that ctDNA contains multiple dominant populations, the evolutionary histories of which frequently indicate whole-genome doubling and shifts in mutational processes. Although tissue and ctDNA showed concordant clonally expanded cancer driver alterations, most individual metastases contributed only a minor share of total ctDNA. By comparing serial ctDNA before and after clinical progression on potent inhibitors of the androgen receptor (AR) pathway, we reveal population restructuring converging solely on AR augmentation as the dominant genomic driver of acquired treatment resistance. Finally, we leverage nucleosome footprints in ctDNA to infer mRNA expression in synchronously biopsied metastases, including treatment-induced changes in AR transcription factor signalling activity. Our results provide insights into cancer biology and show that liquid biopsy can be used as a tool for comprehensive multi-omic discovery.
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Affiliation(s)
- Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Joonatan Sipola
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Sarah W S Ng
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Xinyi E Chen
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Anssi Nurminen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Olga V Korhonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Aslı D Munzur
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elena Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Cecily Q Bernales
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Elie Ritch
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Jack V W Bacon
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | - Nathan A Lack
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,School of Medicine, Koç University, Istanbul, Turkey.,Koç University Research Centre for Translational Medicine, Koç University, Istanbul, Turkey
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Rahul Aggarwal
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Eric J Small
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada
| | | | - David A Quigley
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Epidemiology and Biostatistics, University of California San Francisco, San Francisco, CA, USA
| | - Felix Y Feng
- Helen Diller Family Comprehensive Cancer Center, University of California San Francisco, San Francisco, CA, USA.,Division of Hematology and Oncology, Department of Medicine, University of California San Francisco, San Francisco, CA, USA.,Department of Urology, University of California San Francisco, San Francisco, CA, USA.,Department of Radiation Oncology, University of California San Francisco, San Francisco, CA, USA
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada.,Department of Medical Oncology, BC Cancer, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, British Columbia, Canada. .,Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, British Columbia, Canada.
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22
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L.B. Almeida B, M. Bahrudeen MN, Chauhan V, Dash S, Kandavalli V, Häkkinen A, Lloyd-Price J, S.D. Cristina P, Baptista ISC, Gupta A, Kesseli J, Dufour E, Smolander OP, Nykter M, Auvinen P, Jacobs HT, M.D. Oliveira S, S. Ribeiro A. The transcription factor network of E. coli steers global responses to shifts in RNAP concentration. Nucleic Acids Res 2022; 50:6801-6819. [PMID: 35748858 PMCID: PMC9262627 DOI: 10.1093/nar/gkac540] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/07/2022] [Revised: 06/02/2022] [Accepted: 06/14/2022] [Indexed: 12/24/2022] Open
Abstract
The robustness and sensitivity of gene networks to environmental changes is critical for cell survival. How gene networks produce specific, chronologically ordered responses to genome-wide perturbations, while robustly maintaining homeostasis, remains an open question. We analysed if short- and mid-term genome-wide responses to shifts in RNA polymerase (RNAP) concentration are influenced by the known topology and logic of the transcription factor network (TFN) of Escherichia coli. We found that, at the gene cohort level, the magnitude of the single-gene, mid-term transcriptional responses to changes in RNAP concentration can be explained by the absolute difference between the gene's numbers of activating and repressing input transcription factors (TFs). Interestingly, this difference is strongly positively correlated with the number of input TFs of the gene. Meanwhile, short-term responses showed only weak influence from the TFN. Our results suggest that the global topological traits of the TFN of E. coli shape which gene cohorts respond to genome-wide stresses.
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Affiliation(s)
- Bilena L.B. Almeida
- Correspondence may also be addressed to Bilena L.B. Almeida. Tel: +358 2945211;
| | | | | | | | - Vinodh Kandavalli
- Department of Cell and Molecular Biology, Uppsala University, Uppsala, Sweden
| | - Antti Häkkinen
- Research Program in Systems Oncology, Research Programs Unit, Faculty of Medicine, University of Helsinki, FI-00014 Helsinki, Finland
| | | | - Palma S.D. Cristina
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Ines S C Baptista
- Laboratory of Biosystem Dynamics, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Abhishekh Gupta
- Center for Quantitative Medicine and Department of Cell Biology, University of Connecticut School of Medicine, 263 Farmington Av., Farmington, CT 06030-6033, USA
| | - Juha Kesseli
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Eric Dufour
- Mitochondrial bioenergetics and metabolism, BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Olli-Pekka Smolander
- Department of Chemistry and Biotechnology, Tallinn University of Technology, Tallinn, Estonia
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5D, 00790 Helsinki, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Petri Auvinen
- Institute of Biotechnology, University of Helsinki, Viikinkaari 5D, 00790 Helsinki, Finland
| | - Howard T Jacobs
- Faculty of Medicine and Health Technology, FI-33014 Tampere University, Finland; Department of Environment and Genetics, La Trobe University, Melbourne, Victoria 3086, Australia
| | - Samuel M.D. Oliveira
- Department of Electrical and Computer Engineering, Boston University, Boston, MA, USA
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23
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Sharma M, Aakula A, Tabaro F, Pavic K, Huhtaniemi R, Nykter M, Westermarck J. Abstract 2958: Chromatin repressor complex as a converge point of RAS and PP2A activities in lung cancer. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-2958] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Protein phosphatase 2A (PP2A) is a tumor suppressor while RAS proteins are potent oncogenes in different cancer types. It is well established that RAS-mediated oncogenic transformation requires simultaneous inhibition of PP2A, but the molecular basis of their interaction is poorly understood. To address the target mechanisms co-regulated by RAS and PP2A we performed a phosphoproteomics screen upon RAS or PP2A manipulation. Overall the results indicated that RAS and PP2A regulate overlapping cellular processes, and that their activities might in particular converge at epigenetic machineries.
To study the RAS and PP2A synergy on transcriptional and epigenome regulation we performed multi-omics analysis of cancer cells in which RAS and PP2A activities were modulated. PP2A inhibition resulted in global gene activation while RAS inhibition lead predominantly to gene repression. Use of GFP reporter indicative of epigenetic silencing further confirmed the role of PP2A as a transcriptional repressor and RAS as a transcriptional activator. To investigate the DNA methylation changes and chromatin remodeling effects upon PP2A modulation we used RRBS (Reduced representation bisulfite sequencing) & ATAC-seq (Assay for Transposase-Accessible Chromatin using sequencing) respectively. PP2A inhibition resulted in global DNA hypomethylation and an open state of chromatin confirming its role as a global repressor of epigenetic processes.
To delineate the molecular mechanism behind the transcriptional regulation by RAS and PP2A we monitored the chromatin recruitment of transcriptional repressors upon PP2A or RAS manipulation. Either pharmacological or siRNA mediated PP2A or RAS modulation significantly affected gene repressor complex recruitment to the chromatin. Role of phosphorylation as a critical switch for chromatin repressor complex recruitment was demonstrated by CRISPR/Cas9-mediated mutagenesis of PP2A target phosphorylation site, which also led to a clear phenotype in in vivo tumorigenesis and oncogenic transcription.
Collectively these results identify a novel phosphorylation switch on chromatin repressor complex as a converge point of KRAS and PP2A activities in lung cancer. Generally the results provide first indications to global importance of PP2A-mediated phosphorylation regulation in epigenetic gene regulation in cancer.
Citation Format: Mukund Sharma, Anna Aakula, Francesco Tabaro, Karolina Pavic, Riikka Huhtaniemi, Matti Nykter, Jukka Westermarck. Chromatin repressor complex as a converge point of RAS and PP2A activities in lung cancer [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 2958.
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24
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Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S, Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M, Cremaschi P, Claessens F, Visakorpi T, Tammela TL, Murtola T, Granberg KJ, Lamb AD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A. Abstract 401: Single-cell transcriptome and chromatin sequencing uncover gene expression and gene regulatory patterns associated with enzalutamide resistance. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-401] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Resistance to androgen receptor-targeted therapy due to tumor heterogeneity and clonal evolution is a key challenge for improving prostate cancer outcomes. Despite this, the transcriptomic and chromatin accessibility changes contributing to the emergence of resistance remain incompletely understood at the level of individual cells. Using single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide, we previously identified pre-existing and persistent cell subpopulations that possess regenerative potential when subjected to treatment. Here we analyze the chromatin and transcriptomes of these single cells to characterize their gene regulation and gene expression trajectories. We present evidence of a model of enzalutamide resistance emergence in which the pre-existing and treatment-persistent cells regenerate the bulk of resistant cells. This process is underpinned by chromatin reprogramming that increases the overall relaxation of chromatin upon resistance. We show that the reprogramming of the chromatin further differentially contributes to transcription factor-mediated transcriptional reprogramming via DNA motif exposure in different cell subpopulations. For example, in the treatment-persistent cells, we identify chromatin configurations characterized by the exposure of DNA motifs for GATA2, RELA (a NFkB subunit), CREB1, and E2F1. Pre-existing and treatment-persistent cells consistently display transcriptional features of high developmental potential and RNA velocity analysis identifies them as precursors of cell populations that arise from enzalutamide treatment. We also analyze the pre-existing and treatment-persistent cells in spatial transcriptomics of prostate cancer patient specimens based on their characteristic gene expression profiles. We find these cells to be enriched in cancerous regions of the tissue but also detect them within apparent benign regions, which has potential implications for treatment choice. In summary, we show patterns of gene expression regulation in preclinical models and patient samples that uncover mechanisms of resistance to androgen receptor-targeted therapy in prostate cancer.
Citation Format: Sinja Taavitsainen, Nikolai Engedal, Shaolong Cao, Florian Handle, Andrew Erickson, Stefan Prekovic, Daniel Wetterskog, Teemu Tolonen, Elisa M. Vuorinen, Antti Kiviaho, Reetta Nätkin, Tomi Häkkinen, Wout Devlies, Sallamari Henttinen, Roosa Kaarijärvi, Mari Lahnalampi, Heidi Kaljunen, Karolina Nowakowska, Heimo Syvälä, Merja Bläuer, Paolo Cremaschi, Frank Claessens, Tapio Visakorpi, Teuvo L. Tammela, Teemu Murtola, Kirsi J. Granberg, Alastair D. Lamb, Kirsi Ketola, Ian G. Mills, Gerhardt Attard, Wenyi Wang, Matti Nykter, Alfonso Urbanucci. Single-cell transcriptome and chromatin sequencing uncover gene expression and gene regulatory patterns associated with enzalutamide resistance [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 401.
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Affiliation(s)
| | - Nikolai Engedal
- 2Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Shaolong Cao
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
| | | | | | - Stefan Prekovic
- 6Oncode Institute, The Netherlands Cancer Institute, Amsterdam, Netherlands
| | | | - Teemu Tolonen
- 8Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | | | - Antti Kiviaho
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Reetta Nätkin
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Tomi Häkkinen
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | | | | | | | | | | | | | - Heimo Syvälä
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Merja Bläuer
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Paolo Cremaschi
- 7University College London Cancer Institute, London, United Kingdom
| | | | - Tapio Visakorpi
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | | | - Teemu Murtola
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | | | | | - Kirsi Ketola
- 10University of Eastern Finland, Kuopio, Finland
| | | | - Gerhardt Attard
- 7University College London Cancer Institute, London, United Kingdom
| | - Wenyi Wang
- 3The University of Texas MD Anderson Cancer Center, Houston, TX
| | - Matti Nykter
- 1Tampere University and Tays Cancer Center, Tampere, Finland
| | - Alfonso Urbanucci
- 2Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
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25
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Herberts C, Annala M, Sipola J, Ng SW, Chen XE, Nurminen A, Korhonen O, Munzur AD, Beja K, Schönlau E, Bernales CQ, Ritch E, Bacon JV, Lack NA, Nykter M, Aggarwal R, Small EJ, Gleave ME, Quigley DA, Feng FY, Chi KN, Wyatt AW. Abstract 3625: Clonal architecture and evolution of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing. Cancer Res 2022. [DOI: 10.1158/1538-7445.am2022-3625] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Background: Circulating tumor DNA (ctDNA) in blood plasma is an emerging tool for clinical cancer genotyping and longitudinal disease monitoring. However, integration of ctDNA tests into clinical management is critically impeded by the poor understanding of the distinct somatic populations comprising bulk ctDNA—including their relationship to synchronous metastatic tissue, and their temporal dynamics during standard-of-care treatment. Prior approaches relying on targeted and/or low-resolution techniques (e.g. targeted exon sequencing, low-pass (shallow) whole-genome sequencing; WGS) do not permit comprehensive dissection of clonal architecture and unbiased analysis of putative resistance mechanisms.
Methods: We performed deep WGS on serial plasma ctDNA (median depth: 185×) and synchronous metastatic tissue biopsies with high tumor purity from 35 patients with metastatic castration-resistant prostate cancer. We developed a subclonal reconstruction algorithm optimized for our data enabling resolution of per-patient evolutionary histories and ctDNA clonal composition. ctDNA nucleosome footprinting was used to infer mRNA abundance in synchronously biopsied metastases and androgen receptor (AR) transcription factor activity at 3224 AR binding sites (ARBS).
Results: We comprehensively assess all classes of genomic alterations and demonstrate that ctDNA harbors greater populational heterogeneity than metastatic tissue (p<0.001). The evolutionary histories of ctDNA populations indicate frequent whole-genome doubling and attenuation of C>T aging-associated mutation signature during subclonal differentiation. Although driver alterations were largely concordant between tissue and ctDNA, each individual metastasis contributed only a minor share of total ctDNA (average ctDNA contribution: 17%). By comparing serial ctDNA before and after clinical progression on potent AR pathway inhibitors, we reveal population restructuring converging solely on AR copy augmentation as the dominant genomic driver of acquired treatment-resistance. Nucleosome depletion at transcription start-sites is highly correlated with same-patient metastatic tissue mRNA abundance, indicating that ctDNA fragmentomics can recapitulate transcriptomic patterns in metastatic lesions. Most ctDNA samples exhibited strong ARBS nucleosome depletion which correlated with AR gene copy number (R=0.36, p=0.003). Finally, serial ctDNA nucleosome profiling at ARBS revealed adaptive transcriptomic resistance to AR pathway inhibitors, including lineage switch to a neuroendocrine-like (AR-low) state.
Conclusions: We show that the populations comprising ctDNA are typically complex and more heterogeneous than those found in bulk WGS of a synchronous metastasis. Our work advocates for liquid biopsy as a comprehensive multi-omic discovery tool for cancers with high ctDNA fractions.
Citation Format: Cameron Herberts, Matti Annala, Joonatan Sipola, Sarah W. Ng, Xinyi E. Chen, Anssi Nurminen, Olga Korhonen, Aslı D. Munzur, Kevin Beja, Elena Schönlau, Cecily Q. Bernales, Elie Ritch, Jack V. Bacon, Nathan A. Lack, Matti Nykter, Rahul Aggarwal, Eric J. Small, Martin E. Gleave, David A. Quigley, Felix Y. Feng, Kim N. Chi, Alexander W. Wyatt. Clonal architecture and evolution of treatment-resistant prostate cancer via deep whole-genome ctDNA sequencing [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2022; 2022 Apr 8-13. Philadelphia (PA): AACR; Cancer Res 2022;82(12_Suppl):Abstract nr 3625.
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Affiliation(s)
- Cameron Herberts
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Matti Annala
- 2Tampere University and Tays Cancer Center, Tampere, Finland
| | - Joonatan Sipola
- 2Tampere University and Tays Cancer Center, Tampere, Finland
| | - Sarah W. Ng
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Xinyi E. Chen
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Anssi Nurminen
- 2Tampere University and Tays Cancer Center, Tampere, Finland
| | - Olga Korhonen
- 2Tampere University and Tays Cancer Center, Tampere, Finland
| | - Aslı D. Munzur
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Kevin Beja
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Elena Schönlau
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Elie Ritch
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Jack V. Bacon
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Nathan A. Lack
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | - Matti Nykter
- 2Tampere University and Tays Cancer Center, Tampere, Finland
| | - Rahul Aggarwal
- 3University of California San Francisco, San Francisco, CA
| | - Eric J. Small
- 3University of California San Francisco, San Francisco, CA
| | - Martin E. Gleave
- 1University of British Columbia, Vancouver, British Columbia, Canada
| | | | - Felix Y. Feng
- 3University of California San Francisco, San Francisco, CA
| | - Kim N. Chi
- 4BC Cancer, Vancouver, British Columbia, Canada
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26
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Rodriguez-Martinez A, Vuorinen EM, Shcherban A, Uusi-Mäkelä J, Rajala NKM, Nykter M, Kallioniemi A. Novel ZNF414 activity characterized by integrative analysis of ChIP-exo, ATAC-seq and RNA-seq data. Biochim Biophys Acta Gene Regul Mech 2022; 1865:194811. [PMID: 35318951 DOI: 10.1016/j.bbagrm.2022.194811] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 06/14/2023]
Abstract
Transcription factor binding to DNA is a central mechanism regulating gene expression. Thus, thorough characterization of this process is essential for understanding cellular biology in both health and disease. We combined data from three sequencing-based methods to unravel the DNA binding function of the novel ZNF414 protein in cells representing two tumor types. ChIP-exo served to map protein binding sites, ATAC-seq allowed identification of open chromatin, and RNA-seq examined the transcriptome. We show that ZNF414 is a DNA-binding protein that both induces and represses gene expression. This transcriptional response has an impact on cellular processes related to proliferation and other malignancy-associated functions, such as cell migration and DNA repair. Approximately 20% of the differentially expressed genes harbored ZNF414 binding sites in their promoters in accessible chromatin, likely representing direct targets of ZNF414. De novo motif discovery revealed several putative ZNF414 binding sequences, one of which was validated using EMSA. In conclusion, this study illustrates a highly efficient integrative approach for the characterization of the DNA binding and transcriptional activity of transcription factors.
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Affiliation(s)
- Alejandra Rodriguez-Martinez
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
| | - Elisa M Vuorinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anastasia Shcherban
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Joonas Uusi-Mäkelä
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Nina K M Rajala
- BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anne Kallioniemi
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland; BioMediTech, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Fimlab Laboratories, Tampere, Finland
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27
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Ruusuvuori P, Valkonen M, Kartasalo K, Valkonen M, Visakorpi T, Nykter M, Latonen L. Spatial analysis of histology in 3D: quantification and visualization of organ and tumor level tissue environment. Heliyon 2022; 8:e08762. [PMID: 35128089 PMCID: PMC8800033 DOI: 10.1016/j.heliyon.2022.e08762] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2021] [Revised: 11/24/2021] [Accepted: 01/11/2022] [Indexed: 10/25/2022] Open
Abstract
Histological changes in tissue are of primary importance in pathological research and diagnosis. Automated histological analysis requires ability to computationally separate pathological alterations from normal tissue. Conventional histopathological assessments are performed from individual tissue sections, leading to the loss of three-dimensional context of the tissue. Yet, the tissue context and spatial determinants are critical in several pathologies, such as in understanding growth patterns of cancer in its local environment. Here, we develop computational methods for visualization and quantitative assessment of histopathological alterations in three dimensions. First, we reconstruct the 3D representation of the whole organ from serial sectioned tissue. Then, we proceed to analyze the histological characteristics and regions of interest in 3D. As our example cases, we use whole slide images representing hematoxylin-eosin stained whole mouse prostates in a Pten+/- mouse prostate tumor model. We show that quantitative assessment of tumor sizes, shapes, and separation between spatial locations within the organ enable characterizing and grouping tumors. Further, we show that 3D visualization of tissue with computationally quantified features provides an intuitive way to observe tissue pathology. Our results underline the heterogeneity in composition and cellular organization within individual tumors. As an example, we show how prostate tumors have nuclear density gradients indicating areas of tumor growth directions and reflecting varying pressure from the surrounding tissue. The methods presented here are applicable to any tissue and different types of pathologies. This work provides a proof-of-principle for gaining a comprehensive view from histology by studying it quantitatively in 3D.
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Affiliation(s)
- Pekka Ruusuvuori
- Institute of Biomedicine, University of Turku, Turku, Finland
- Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Masi Valkonen
- Institute of Biomedicine, University of Turku, Turku, Finland
| | - Kimmo Kartasalo
- Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Mira Valkonen
- Faculty of Medicine and Health Technology, Tampere University, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
- Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University, Finland
- Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
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28
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Ketola K, Kaljunen H, Taavitsainen S, Kaarijärvi R, Järvelä E, Rodríguez-Martín B, Haase K, Woodcock DJ, Tubio J, Wedge DC, Nykter M, Bova GS. Subclone Eradication Analysis Identifies Targets for Enhanced Cancer Therapy and Reveals L1 Retrotransposition as a Dynamic Source of Cancer Heterogeneity. Cancer Res 2021; 81:4901-4909. [PMID: 34348967 PMCID: PMC9397610 DOI: 10.1158/0008-5472.can-21-0371] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2021] [Revised: 06/03/2021] [Accepted: 08/02/2021] [Indexed: 01/07/2023]
Abstract
Treatment-eradicated cancer subclones have been reported in leukemia and have recently been detected in solid tumors. Here we introduce Differential Subclone Eradication and Resistance (DSER) analysis, a method developed to identify molecular targets for improved therapy by direct comparison of genomic features of eradicated and resistant subclones in pre- and posttreatment samples from a patient with BRCA2-deficient metastatic prostate cancer. FANCI and EYA4 were identified as candidate DNA repair-related targets for converting subclones from resistant to eradicable, and RNAi-mediated depletion of FANCI confirmed it as a potential target. The EYA4 alteration was associated with adjacent L1 transposon insertion during cancer evolution upon treatment, raising questions surrounding the role of therapy in L1 activation. Both carboplatin and enzalutamide turned on L1 transposon machinery in LNCaP and VCaP but not in PC3 and 22Rv1 prostate cancer cell lines. L1 activation in LNCaP and VCaP was inhibited by the antiretroviral drug azidothymidine. L1 activation was also detected postcastration in LuCaP 77 and LuCaP 105 xenograft models and postchemotherapy in previously published time-series transcriptomic data from SCC25 head and neck cancer cells. In conclusion, DSER provides an informative intermediate step toward effective precision cancer medicine and should be tested in future studies, especially those including dramatic but temporary metastatic tumor regression. L1 transposon activation may be a modifiable source of cancer genomic heterogeneity, suggesting the potential of leveraging newly discovered triggers and blockers of L1 activity to overcome therapy resistance. SIGNIFICANCE: Differential analysis of eradicated and resistant subclones following cancer treatment identifies that L1 activity associated with resistance is induced by current therapies and blocked by the antiretroviral drug azidothymidine.
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Affiliation(s)
- Kirsi Ketola
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland.,Corresponding Authors: Kirsi Ketola, Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, Kuopio FI-70211, Finland. Phone: 358-503299984; E-mail: ; and G. S. Bova, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, PO Box 100, Tampere FI-33014, Finland. Phone: 358-502945211; E-mail:
| | - Heidi Kaljunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - Roosa Kaarijärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Emmi Järvelä
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Bernardo Rodríguez-Martín
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - Kerstin Haase
- Experimental and Clinical Research Center, Charité and the Max Delbrück Center for Molecular Medicine, Universitätsmedizin Berlin, Berlin, Germany
| | - Dan J. Woodcock
- Big Data Institute, University of Oxford, Li Ka Shing Centre for Health Information and Discovery, Oxford, United Kingdom
| | - Jose Tubio
- Genomes and Disease, Centre for Research in Molecular Medicine and Chronic Diseases (CIMUS), Universidade de Santiago de Compostela, Santiago de Compostela, Spain.,Department of Zoology, Genetics and Physical Anthropology, Universidade de Santiago de Compostela, Santiago de Compostela, Spain
| | - David C. Wedge
- Manchester Cancer Research Centre, University of Manchester, Manchester, United Kingdom
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.,Corresponding Authors: Kirsi Ketola, Institute of Biomedicine, University of Eastern Finland, P.O. Box 1627, Kuopio FI-70211, Finland. Phone: 358-503299984; E-mail: ; and G. S. Bova, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, PO Box 100, Tampere FI-33014, Finland. Phone: 358-502945211; E-mail:
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29
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Jacome Sanz D, Saralahti AK, Pekkarinen M, Kesseli J, Nykter M, Rämet M, Ojanen MJT, Pesu M. Proprotein convertase subtilisin/kexin type 9 regulates the production of acute-phase reactants from the liver. Liver Int 2021; 41:2511-2522. [PMID: 34174143 DOI: 10.1111/liv.14993] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/07/2021] [Revised: 06/07/2021] [Accepted: 06/24/2021] [Indexed: 12/13/2022]
Abstract
BACKGROUND & AIMS Proprotein convertase subtilisin/kexin type 9 (PCSK9) controls blood cholesterol levels by fostering the LDL receptor (LDLR) degradation in hepatocytes. Additionally, PCSK9 has been suggested to participate in immunoregulation by modulating cytokine production. We studied the immunological role of PCSK9 in Streptococcus pneumoniae bacteraemia in vivo and in a human hepatocyte cell line. METHODS CRISPR/Cas9 mutagenesis was utilized to create pcsk9 knock-out (KO) zebrafish, which were infected with S pneumoniae to assess the role of PCSK9 for the survival of the fish and in the transcriptomic response of the liver. The direct effects of PCSK9 on the expression of acute-phase reaction (APR) genes were studied in HepG2 cells. RESULTS The pcsk9 KO zebrafish lines (pcsk9tpu-13 and pcsk9tpu-2,+15 ) did not show developmental defects or gross phenotypical differences. In the S pneumoniae infected zebrafish, the mortality of pcsk9 KOs was similar to the controls. A liver-specific gene expression analysis revealed that a pneumococcal challenge upregulated pcsk9, and that the pcsk9 deletion reduced the expression of APR genes, including hepcidin antimicrobial peptide (hamp) and complement component 7b (c7b). Accordingly, silencing PCSK9 in vitro in HepG2 cells using small interfering RNAs (siRNAs) decreased HAMP expression. CONCLUSIONS We demonstrate that PCSK9 is not critical for zebrafish survival in a systemic pneumococcal infection. However, PCSK9 deficiency was associated with the lower expression of APR genes in zebrafish and altered the expression of innate immunity genes in a human hepatocyte cell line. Overall, our data suggest an evolutionarily conserved function for PCSK9 in APR in the liver.
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Affiliation(s)
- Dafne Jacome Sanz
- Laboratory of Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Anni K Saralahti
- Laboratory of Experimental Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Meeri Pekkarinen
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Juha Kesseli
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Matti Nykter
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Mika Rämet
- Laboratory of Experimental Immunology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Vaccine Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,PEDEGO Research Unit, Medical Research Center, University of Oulu, Oulu, Finland.,Department of Children and Adolescents, Oulu University Hospital, Oulu, Finland
| | - Markus J T Ojanen
- Laboratory of Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Marko Pesu
- Laboratory of Immunoregulation, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.,Fimlab laboratories Ltd, Tampere, Finland
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30
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Taavitsainen S, Engedal N, Cao S, Handle F, Erickson A, Prekovic S, Wetterskog D, Tolonen T, Vuorinen EM, Kiviaho A, Nätkin R, Häkkinen T, Devlies W, Henttinen S, Kaarijärvi R, Lahnalampi M, Kaljunen H, Nowakowska K, Syvälä H, Bläuer M, Cremaschi P, Claessens F, Visakorpi T, Tammela TLJ, Murtola T, Granberg KJ, Lamb AD, Ketola K, Mills IG, Attard G, Wang W, Nykter M, Urbanucci A. Single-cell ATAC and RNA sequencing reveal pre-existing and persistent cells associated with prostate cancer relapse. Nat Commun 2021; 12:5307. [PMID: 34489465 PMCID: PMC8421417 DOI: 10.1038/s41467-021-25624-1] [Citation(s) in RCA: 46] [Impact Index Per Article: 15.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/01/2021] [Accepted: 08/23/2021] [Indexed: 02/08/2023] Open
Abstract
Prostate cancer is heterogeneous and patients would benefit from methods that stratify those who are likely to respond to systemic therapy. Here, we employ single-cell assays for transposase-accessible chromatin (ATAC) and RNA sequencing in models of early treatment response and resistance to enzalutamide. In doing so, we identify pre-existing and treatment-persistent cell subpopulations that possess regenerative potential when subjected to treatment. We find distinct chromatin landscapes associated with enzalutamide treatment and resistance that are linked to alternative transcriptional programs. Transcriptional profiles characteristic of persistent cells are able to stratify the treatment response of patients. Ultimately, we show that defining changes in chromatin and gene expression in single-cell populations from pre-clinical models can reveal as yet unrecognized molecular predictors of treatment response. This suggests that the application of single-cell methods with high analytical resolution in pre-clinical models may powerfully inform clinical decision-making.
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Affiliation(s)
- S Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - N Engedal
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - S Cao
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - F Handle
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Urology, Division of Experimental Urology, Medical University of Innsbruck, Innsbruck, Austria
| | - A Erickson
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
| | - S Prekovic
- Division of Oncogenomics, Oncode Institute, The Netherlands Cancer Institute, Amsterdam, The Netherlands
| | - D Wetterskog
- University College London Cancer Institute, London, UK
| | - T Tolonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital, Tampere, Finland
| | - E M Vuorinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - A Kiviaho
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - R Nätkin
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - T Häkkinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - W Devlies
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
- Department of Urology, UZ Leuven, Leuven, Belgium
| | - S Henttinen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - R Kaarijärvi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - M Lahnalampi
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - H Kaljunen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - K Nowakowska
- University College London Cancer Institute, London, UK
| | - H Syvälä
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - M Bläuer
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - P Cremaschi
- University College London Cancer Institute, London, UK
| | - F Claessens
- Molecular Endocrinology Laboratory, Department of Cellular and Molecular Medicine, KU Leuven, Leuven, Belgium
| | - T Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
- Fimlab Laboratories, Ltd, Tampere University Hospital, Tampere, Finland
| | - T L J Tammela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - T Murtola
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - K J Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland
| | - A D Lamb
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Department of Urology, Churchill Hospital Cancer Centre, Oxford, UK
| | - K Ketola
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - I G Mills
- Nuffield Department of Surgical Sciences, University of Oxford, Oxford, UK
- Patrick G Johnston Centre for Cancer Research, Queen's University of Belfast, Belfast, UK
- Centre for Cancer Biomarkers (CCBIO), University of Bergen, Bergen, Norway
| | - G Attard
- University College London Cancer Institute, London, UK
| | - W Wang
- Department of Bioinformatics and Computational Biology, The University of Texas MD Anderson Cancer Center, Houston, TX, USA
| | - M Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere, Finland.
| | - A Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.
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31
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Rajamäki K, Taira A, Katainen R, Välimäki N, Kuosmanen A, Plaketti RM, Seppälä TT, Ahtiainen M, Wirta EV, Vartiainen E, Sulo P, Ravantti J, Lehtipuro S, Granberg KJ, Nykter M, Tanskanen T, Ristimäki A, Koskensalo S, Renkonen-Sinisalo L, Lepistö A, Böhm J, Taipale J, Mecklin JP, Aavikko M, Palin K, Aaltonen LA. Genetic and Epigenetic Characteristics of Inflammatory Bowel Disease-Associated Colorectal Cancer. Gastroenterology 2021; 161:592-607. [PMID: 33930428 DOI: 10.1053/j.gastro.2021.04.042] [Citation(s) in RCA: 63] [Impact Index Per Article: 21.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Revised: 04/16/2021] [Accepted: 04/16/2021] [Indexed: 02/07/2023]
Abstract
BACKGROUND & AIMS Inflammatory bowel disease (IBD) is a chronic, relapsing inflammatory disorder associated with an elevated risk of colorectal cancer (CRC). IBD-associated CRC (IBD-CRC) may represent a distinct pathway of tumorigenesis compared to sporadic CRC (sCRC). Our aim was to comprehensively characterize IBD-associated tumorigenesis integrating multiple high-throughput approaches, and to compare the results with in-house data sets from sCRCs. METHODS Whole-genome sequencing, single nucleotide polymorphism arrays, RNA sequencing, genome-wide methylation analysis, and immunohistochemistry were performed using fresh-frozen and formalin-fixed tissue samples of tumor and corresponding normal tissues from 31 patients with IBD-CRC. RESULTS Transcriptome-based tumor subtyping revealed the complete absence of canonical epithelial tumor subtype associated with WNT signaling in IBD-CRCs, dominated instead by mesenchymal stroma-rich subtype. Negative WNT regulators AXIN2 and RNF43 were strongly down-regulated in IBD-CRCs and chromosomal gains at HNF4A, a negative regulator of WNT-induced epithelial-mesenchymal transition (EMT), were less frequent compared to sCRCs. Enrichment of hypomethylation at HNF4α binding sites was detected solely in sCRC genomes. PIGR and OSMR involved in mucosal immunity were dysregulated via epigenetic modifications in IBD-CRCs. Genome-wide analysis showed significant enrichment of noncoding mutations to 5'untranslated region of TP53 in IBD-CRCs. As reported previously, somatic mutations in APC and KRAS were less frequent in IBD-CRCs compared to sCRCs. CONCLUSIONS Distinct mechanisms of WNT pathway dysregulation skew IBD-CRCs toward mesenchymal tumor subtype, which may affect prognosis and treatment options. Increased OSMR signaling may favor the establishment of mesenchymal tumors in patients with IBD.
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Affiliation(s)
- Kristiina Rajamäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.
| | - Aurora Taira
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Riku Katainen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Niko Välimäki
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Anna Kuosmanen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Roosa-Maria Plaketti
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Toni T Seppälä
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Surgery, Helsinki University Central Hospital and University of Helsinki, Helsinki, Finland; Department of Surgical Oncology, Johns Hopkins University, Baltimore, Maryland
| | - Maarit Ahtiainen
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | - Erkki-Ville Wirta
- Department of Gastroenterology and Alimentary Tract Surgery, Tampere University Hospital, Tampere, Finland
| | - Emilia Vartiainen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Päivi Sulo
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Janne Ravantti
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Suvi Lehtipuro
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Kirsi J Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland; Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tomas Tanskanen
- Finnish Cancer Registry, Institute for Statistical and Epidemiological Cancer Research, Helsinki, Finland
| | - Ari Ristimäki
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Department of Pathology, HUSLAB, HUS Diagnostic Center, University of Helsinki and Helsinki University Hospital, Helsinki, Finland
| | - Selja Koskensalo
- Department of Gastrointestinal Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Laura Renkonen-Sinisalo
- Department of Gastrointestinal Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Anna Lepistö
- Department of Gastrointestinal Surgery, Helsinki University Hospital and University of Helsinki, Helsinki, Finland
| | - Jan Böhm
- Department of Pathology, Central Finland Health Care District, Jyväskylä, Finland
| | - Jussi Taipale
- Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Division of Functional Genomics and Systems Biology, Department of Medical Biochemistry and Biophysics, Karolinska Institutet, Stockholm, Sweden; Department of Biochemistry, University of Cambridge, Cambridge, UK
| | - Jukka-Pekka Mecklin
- Sport and Health Sciences, University of Jyväskylä, Jyväskylä, Finland; Department of Education and Research, Central Finland Central Hospital, Jyväskylä, Finland
| | - Mervi Aavikko
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland; Institute for Molecular Medicine Finland, HiLIFE, University of Helsinki, Helsinki, Finland
| | - Kimmo Palin
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland
| | - Lauri A Aaltonen
- Department of Medical and Clinical Genetics, University of Helsinki, Helsinki, Finland; Applied Tumor Genomics Research Program, Research Programs Unit, University of Helsinki, Helsinki, Finland.
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32
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Jasu J, Tolonen T, Antonarakis ES, Beltran H, Halabi S, Eisenberger MA, Carducci MA, Loriot Y, Van der Eecken K, Lolkema M, Ryan CJ, Taavitsainen S, Gillessen S, Högnäs G, Talvitie T, Taylor RJ, Koskenalho A, Ost P, Murtola TJ, Rinta-Kiikka I, Tammela T, Auvinen A, Kujala P, Smith TJ, Kellokumpu-Lehtinen PL, Isaacs WB, Nykter M, Kesseli J, Bova GS. Combined Longitudinal Clinical and Autopsy Phenomic Assessment in Lethal Metastatic Prostate Cancer: Recommendations for Advancing Precision Medicine. EUR UROL SUPPL 2021; 30:47-62. [PMID: 34337548 PMCID: PMC8317817 DOI: 10.1016/j.euros.2021.05.011] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2021] [Indexed: 12/23/2022] Open
Abstract
BACKGROUND Systematic identification of data essential for outcome prediction in metastatic prostate cancer (mPC) would accelerate development of precision oncology. OBJECTIVE To identify novel phenotypes and features associated with mPC outcome, and to identify biomarker and data requirements to be tested in future precision oncology trials. DESIGN SETTING AND PARTICIPANTS We analyzed deep longitudinal clinical, neuroendocrine expression, and autopsy data of 33 men who died from mPC between 1995 and 2004 (PELICAN33), and related findings to mPC biomarkers reported in the literature. INTERVENTION Thirty-three men prospectively consented to participate in an integrated clinical-molecular rapid autopsy study of mPC. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS Data exploration with correction for multiple testing and survival analysis from the time of diagnosis to time to death and time to first occurrence of severe pain as outcomes were carried out. The effect of seven complications on the modeled probability of dying within 2 yr after presenting with the complication was evaluated using logistic regression. RESULTS AND LIMITATIONS Feature exploration revealed novel phenotypes related to mPC outcome. Four complications (pleural effusion, severe anemia, severe or controlled pain, and bone fracture) predict the likelihood of death within 2 yr. Men with Gleason grade group 5 cancers developed severe pain sooner than those with lower-grade tumors. Surprisingly, neuroendocrine (NE) differentiation was frequently observed in the setting of high serum prostate-specific antigen (PSA) levels (≥30 ng/ml). In 4/33 patients, no controlled (requiring analgesics) or severe pain was detected, and strikingly, 14/15 metastatic sites studied in these men did not express NE markers, suggesting an inverse relationship between NE differentiation and pain in mPC. Intracranial subdural metastasis is common (36%) and is usually clinically undetected. Categorization of "skeletal-related events" complications used in recent studies likely obscures the understanding of spinal cord compression and fracture. Early death from prostate cancer was identified in a subgroup of men with a low longitudinal PSA bandwidth. Cachexia is common (body mass index <0.89 in 24/31 patients) but limited to the last year of life. Biomarker review identified 30 categories of mPC biomarkers in need of winnowing in future trials. All findings require validation in larger cohorts, preferably alongside data from this study. CONCLUSIONS The study identified novel outcome subgroups for future validation and provides "vision for mPC precision oncology 2020-2050" draft recommendations for future data collection and biomarker studies. PATIENT SUMMARY To better understand variation in metastatic prostate cancer behavior, we assembled and analyzed longitudinal clinical and autopsy records in 33 men. We identified novel outcomes, phenotypes, and aspects of disease burden to be tested and refined in future trials.
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Affiliation(s)
- Juho Jasu
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Teemu Tolonen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Emmanuel S. Antonarakis
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | | | - Susan Halabi
- Duke University Medical Center, Department of Biostatistics and Bioinformatics, Durham, NC, USA
| | - Mario A. Eisenberger
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Michael A. Carducci
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Yohann Loriot
- Department of Medical Oncology, Gustave Roussy, Villejuif, France
| | - Kim Van der Eecken
- Department of Medical and Forensic Pathology, Ghent University, Ghent, Belgium
| | - Martijn Lolkema
- Department of Medical Oncology, Erasmus Medical Center, Rotterdam, The Netherlands
| | - Charles J. Ryan
- Department of Medicine, Division of Oncology, University of Minnesota, Minneapolis, MN, USA
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Silke Gillessen
- Institute of Oncology of Southern Switzerland, Bellinzona, Switzerland
- Faculty of Biosciences, Università della Svizzera Italiana, Lugano, Switzerland
- Faculty of Cancer Science, University of Manchester, UK
| | - Gunilla Högnäs
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Timo Talvitie
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | | | - Antti Koskenalho
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Piet Ost
- Department of Radiation Oncology, Iridium Netwerk, Wilrijk (Antwerp), Belgium
- Department of Human Structure and Repair, Ghent University, Ghent, Belgium
| | - Teemu J. Murtola
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- TAYS Cancer Center, Department of Urology, Tampere, Finland
| | - Irina Rinta-Kiikka
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- TAYS Cancer Center, Department of Radiology, Tampere, Finland
| | - Teuvo Tammela
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- TAYS Cancer Center, Department of Urology, Tampere, Finland
| | - Anssi Auvinen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
- Faculty of Social Sciences, Unit of Health Sciences, Tampere University, Tampere, Finland
| | - Paula Kujala
- Fimlab Laboratories, Department of Pathology, Tampere University Hospital, Tampere, Finland
| | - Thomas J. Smith
- Department of Oncology, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
- Department of Medicine, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Pirkko-Liisa Kellokumpu-Lehtinen
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - William B. Isaacs
- Brady Urological Institute, Johns Hopkins University School of Medicine, Baltimore, MD 21287, USA
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
| | - G. Steven Bova
- Faculty of Medicine and Health Technology, Prostate Cancer Research Center, Tampere University and Tays Cancer Center, Tampere, FI-33014, Finland
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Kukkonen K, Taavitsainen S, Huhtala L, Uusi-Makela J, Granberg KJ, Nykter M, Urbanucci A. Chromatin and Epigenetic Dysregulation of Prostate Cancer Development, Progression, and Therapeutic Response. Cancers (Basel) 2021; 13:3325. [PMID: 34283056 PMCID: PMC8268970 DOI: 10.3390/cancers13133325] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2021] [Revised: 06/25/2021] [Accepted: 06/29/2021] [Indexed: 02/07/2023] Open
Abstract
The dysregulation of chromatin and epigenetics has been defined as the overarching cancer hallmark. By disrupting transcriptional regulation in normal cells and mediating tumor progression by promoting cancer cell plasticity, this process has the ability to mediate all defined hallmarks of cancer. In this review, we collect and assess evidence on the contribution of chromatin and epigenetic dysregulation in prostate cancer. We highlight important mechanisms leading to prostate carcinogenesis, the emergence of castration-resistance upon treatment with androgen deprivation therapy, and resistance to antiandrogens. We examine in particular the contribution of chromatin structure and epigenetics to cell lineage commitment, which is dysregulated during tumorigenesis, and cell plasticity, which is altered during tumor progression.
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Affiliation(s)
- Konsta Kukkonen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Sinja Taavitsainen
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Laura Huhtala
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Joonas Uusi-Makela
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Kirsi J. Granberg
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Matti Nykter
- Prostate Cancer Research Center, Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, 33520 Tampere, Finland; (K.K.); (S.T.); (L.H.); (J.U.-M.); (K.J.G.); (M.N.)
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway
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34
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Annala M, Taavitsainen S, Khalaf DJ, Vandekerkhove G, Beja K, Sipola J, Warner EW, Herberts C, Wong A, Fu S, Finch DL, Oja CD, Vergidis J, Zulfiqar M, Eigl BJ, Kollmansberger CK, Nykter M, Gleave ME, Chi KN, Wyatt AW. Evolution of Castration-Resistant Prostate Cancer in ctDNA during Sequential Androgen Receptor Pathway Inhibition. Clin Cancer Res 2021; 27:4610-4623. [PMID: 34083234 DOI: 10.1158/1078-0432.ccr-21-1625] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2021] [Revised: 05/21/2021] [Accepted: 06/01/2021] [Indexed: 11/16/2022]
Abstract
PURPOSE Cross-resistance renders multiple lines of androgen receptor (AR) signaling inhibitors increasingly futile in metastatic castration-resistant prostate cancer (mCRPC). We sought to determine acquired genomic contributors to cross-resistance. EXPERIMENTAL DESIGN We collected 458 serial plasma cell-free DNA samples at baseline and progression timepoints from 202 patients with mCRPC receiving sequential AR signaling inhibitors (abiraterone and enzalutamide) in a randomized phase II clinical trial (NCT02125357). We utilized deep targeted and whole-exome sequencing to compare baseline and posttreatment somatic genomic profiles in circulating tumor DNA (ctDNA). RESULTS Patient ctDNA abundance was correlated across plasma collections and independently prognostic for sequential therapy response and overall survival. Most driver alterations in established prostate cancer genes were consistently detected in ctDNA over time. However, shifts in somatic populations after treatment were identified in 53% of patients, particularly after strong treatment responses. Treatment-associated changes converged upon the AR gene, with an average 50% increase in AR copy number, changes in AR mutation frequencies, and a 2.5-fold increase in the proportion of patients carrying AR ligand binding domain truncating rearrangements. CONCLUSIONS Our data show that the dominant AR genotype continues to evolve during sequential lines of AR inhibition and drives acquired resistance in patients with mCRPC.
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Affiliation(s)
- Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada.,Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Daniel J Khalaf
- BC Cancer, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Gillian Vandekerkhove
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Kevin Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Joonatan Sipola
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Evan W Warner
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Amanda Wong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Simon Fu
- BC Cancer, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Daygen L Finch
- BC Cancer, Southern Interior Centre, Kelowna, British Columbia, Canada
| | - Conrad D Oja
- BC Cancer, Fraser Valley Centre, Vancouver, British Columbia, Canada
| | - Joanna Vergidis
- BC Cancer, Vancouver Island Centre, Victoria, British Columbia, Canada
| | | | - Bernhard J Eigl
- BC Cancer, Vancouver Centre, Vancouver, British Columbia, Canada
| | | | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada. .,BC Cancer, Vancouver Centre, Vancouver, British Columbia, Canada
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, British Columbia, Canada.
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35
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Cerqueira JXM, Saavalainen P, Kurppa K, Laurikka P, Huhtala H, Nykter M, L E Koskinen L, Yohannes DA, Kilpeläinen E, Shcherban A, Palotie A, Kaukinen K, Lindfors K. Independent and cumulative coeliac disease-susceptibility loci are associated with distinct disease phenotypes. J Hum Genet 2021; 66:613-623. [PMID: 33446885 PMCID: PMC8144013 DOI: 10.1038/s10038-020-00888-5] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 12/12/2022]
Abstract
The phenotype of coeliac disease varies considerably for incompletely understood reasons. We investigated whether established coeliac disease susceptibility variants (SNPs) are individually or cumulatively associated with distinct phenotypes. We also tested whether a polygenic risk score (PRS) based on genome-wide associated (GWA) data could explain the phenotypic variation. The phenotypic association of 39 non-HLA coeliac disease SNPs was tested in 625 thoroughly phenotyped coeliac disease patients and 1817 controls. To assess their cumulative effects a weighted genetic risk score (wGRS39) was built, and stratified by tertiles. In our PRS model in cases, we took the summary statistics from the largest GWA study in coeliac disease and tested their association at eight P value thresholds (PT) with phenotypes. Altogether ten SNPs were associated with distinct phenotypes after correction for multiple testing (PEMP2 ≤ 0.05). The TLR7/TLR8 locus was associated with disease onset before and the SH2B3/ATXN2, ITGA4/UBE2E3 and IL2/IL21 loci after 7 years of age. The latter three loci were associated with a more severe small bowel mucosal damage and SH2B3/ATXN2 with type 1 diabetes. Patients at the highest wGRS39 tertiles had OR > 1.62 for having coeliac disease-related symptoms during childhood, a more severe small bowel mucosal damage, malabsorption and anaemia. PRS was associated only with dermatitis herpetiformis (PT = 0.2, PEMP2 = 0.02). Independent coeliac disease-susceptibility loci are associated with distinct phenotypes, suggesting that genetic factors play a role in determining the disease presentation. Moreover, the increased number of coeliac disease susceptibility SNPs might predispose to a more severe disease course.
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Affiliation(s)
- Juliana X M Cerqueira
- Coeliac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Päivi Saavalainen
- Research Programs Unit, Immunobiology, and the Haartman Institute, Department of Molecular Genetics, University of Helsinki, Helsinki, Finland
| | - Kalle Kurppa
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, and the University Consortium of Seinäjoki, Seinäjoki, Finland
| | - Pilvi Laurikka
- Coeliac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Heini Huhtala
- Faculty of Social Sciences, Tampere University, Tampere, Finland
| | - Matti Nykter
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Lotta L E Koskinen
- Research Programs Unit, Immunobiology, and the Haartman Institute, Department of Molecular Genetics, University of Helsinki, Helsinki, Finland
| | - Dawit A Yohannes
- Research Programs Unit, Immunobiology, and the Haartman Institute, Department of Molecular Genetics, University of Helsinki, Helsinki, Finland
| | - Elina Kilpeläinen
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Anastasia Shcherban
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
| | - Aarno Palotie
- Institute for Molecular Medicine Finland (FIMM), University of Helsinki, Helsinki, Finland
- Broad Institute of the Massachusetts Institute of Technology and Harvard University, Cambridge, MA, USA
- Psychiatric & Neurodevelopmental Genetics Unit, Department of Psychiatry, Analytic and Translational Genetics Unit, Department of Medicine, and the Department of Neurology, Massachusetts General Hospital, Boston, MA, USA
| | - Katri Kaukinen
- Coeliac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Department of Internal Medicine, Tampere University Hospital, Tampere, Finland
| | - Katri Lindfors
- Coeliac Disease Research Center, Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland.
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36
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Filppu P, Tanjore Ramanathan J, Granberg KJ, Gucciardo E, Haapasalo H, Lehti K, Nykter M, Le Joncour V, Laakkonen P. CD109-GP130 interaction drives glioblastoma stem cell plasticity and chemoresistance through STAT3 activity. JCI Insight 2021; 6:141486. [PMID: 33986188 PMCID: PMC8262342 DOI: 10.1172/jci.insight.141486] [Citation(s) in RCA: 19] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2020] [Accepted: 04/01/2021] [Indexed: 12/21/2022] Open
Abstract
Glioma stem cells (GSCs) drive propagation and therapeutic resistance of glioblastomas, the most aggressive diffuse brain tumors. However, the molecular mechanisms that maintain the stemness and promote therapy resistance remain poorly understood. Here we report CD109/STAT3 axis as crucial for the maintenance of stemness and tumorigenicity of GSCs and as a mediator of chemoresistance. Mechanistically, CD109 physically interacts with glycoprotein 130 to promote activation of the IL-6/STAT3 pathway in GSCs. Genetic depletion of CD109 abolished the stemness and self-renewal of GSCs and impaired tumorigenicity. Loss of stemness was accompanied with a phenotypic shift of GSCs to more differentiated astrocytic-like cells. Importantly, genetic or pharmacologic targeting of CD109/STAT3 axis sensitized the GSCs to chemotherapy, suggesting that targeting CD109/STAT3 axis has potential to overcome therapy resistance in glioblastoma.
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Affiliation(s)
- Pauliina Filppu
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | | | - Kirsi J. Granberg
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
- Science Center, Tampere University Hospital, Tampere, Finland
| | - Erika Gucciardo
- Individualized Drug Therapy Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Hannu Haapasalo
- Department of Pathology, Fimlab Laboratories, Tampere University Hospital and University of Tampere, Tampere, Finland
| | - Kaisa Lehti
- Individualized Drug Therapy Program, Research Programs Unit, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Department of Microbiology, Tumor and Cell Biology, Karolinska Institutet, Stockholm, Sweden
- Department of Biomedical Laboratory Science, Faculty of Natural Sciences, Norwegian University of Science and Technology, Trondheim, Norway
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University, Tampere, Finland
| | - Vadim Le Joncour
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Pirjo Laakkonen
- Translational Cancer Medicine Research Program, Faculty of Medicine, University of Helsinki, Helsinki, Finland
- Laboratory Animal Centre, Helsinki Institute of Life Science (HiLIFE), University of Helsinki, Helsinki, Finland
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37
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Cangiano M, Grudniewska M, Salji MJ, Nykter M, Jenster G, Urbanucci A, Granchi Z, Janssen B, Hamilton G, Leung HY, Beumer IJ. Gene Regulation Network Analysis on Human Prostate Orthografts Highlights a Potential Role for the JMJD6 Regulon in Clinical Prostate Cancer. Cancers (Basel) 2021; 13:cancers13092094. [PMID: 33925994 PMCID: PMC8123677 DOI: 10.3390/cancers13092094] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/01/2021] [Revised: 04/09/2021] [Accepted: 04/21/2021] [Indexed: 02/06/2023] Open
Abstract
Simple Summary Prostate cancer is a very common malignancy worldwide. Treatment resistant prostate cancer poses a big challenge to clinicians and is the second most common cause of premature death in men with cancer. Gene expression analysis has been performed on clinical tumours but to date none of the gene expression-based biomarkers for prostate cancer have been successfully integrated to into clinical practice to improve patient management and treatment choice. We applied a novel laboratory prostate cancer model to mimic clinical hormone responsive and resistant prostate cancer and tested whether a network of genes similarly regulated by transcription factors (gene products that control the expression of target genes) are associated with patient outcome. We identified regulons (networks of genes similarly regulated) from our preclinical prostate cancer models and further evaluated the top ranked JMJD6 gene related regulated network in three independent clinical patient cohorts. Abstract Background: Prostate cancer (PCa) is the second most common tumour diagnosed in men. Tumoral heterogeneity in PCa creates a significant challenge to develop robust prognostic markers and novel targets for therapy. An analysis of gene regulatory networks (GRNs) in PCa may provide insight into progressive PCa. Herein, we exploited a graph-based enrichment score to integrate data from GRNs identified in preclinical prostate orthografts and differentially expressed genes in clinical resected PCa. We identified active regulons (transcriptional regulators and their targeted genes) associated with PCa recurrence following radical prostatectomy. Methods: The expression of known transcription factors and co-factors was analysed in a panel of prostate orthografts (n = 18). We searched for genes (as part of individual GRNs) predicted to be regulated by the highest number of transcriptional factors. Using differentially expressed gene analysis (on a per sample basis) coupled with gene graph enrichment analysis, we identified candidate genes and associated GRNs in PCa within the UTA cohort, with the most enriched regulon being JMJD6, which was further validated in two additional cohorts, namely EMC and ICGC cohorts. Cox regression analysis was performed to evaluate the association of the JMJD6 regulon activity with disease-free survival time in the three clinical cohorts as well as compared to three published prognostic gene signatures (TMCC11, BROMO-10 and HYPOXIA-28). Results: 1308 regulons were correlated to transcriptomic data from the three clinical prostatectomy cohorts. The JMJD6 regulon was identified as the top enriched regulon in the UTA cohort and again validated in the EMC cohort as the top-ranking regulon. In both UTA and EMC cohorts, the JMJD6 regulon was significantly associated with cancer recurrence. Active JMJD6 regulon also correlated with disease recurrence in the ICGC cohort. Furthermore, Kaplan–Meier analysis confirmed shorter time to recurrence in patients with active JMJD6 regulon for all three clinical cohorts (UTA, EMC and ICGC), which was not the case for three published prognostic gene signatures (TMCC11, BROMO-10 and HYPOXIA-28). In multivariate analysis, the JMJD6 regulon status significantly predicted disease recurrence in the UTA and EMC, but not ICGC datasets, while none of the three published signatures significantly prognosticate for cancer recurrence. Conclusions: We have characterised gene regulatory networks from preclinical prostate orthografts and applied transcriptomic data from three clinical cohorts to evaluate the prognostic potential of the JMJD6 regulon.
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Affiliation(s)
- Mario Cangiano
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
| | - Magda Grudniewska
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
| | - Mark J. Salji
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK;
- CRUK Beatson Institute, Glasgow G61 1BD, UK
| | - Matti Nykter
- Laboratory of Computational Biology, Institute of Biomedical Technology, Arvo Ylpön katu 34, 33520 Tampere, Finland;
| | - Guido Jenster
- Department of Urology, Erasmus Medical Center, Doctor Molewaterplein 40, 3015 GD Rotterdam, The Netherlands;
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, 0424 Oslo, Norway;
| | - Zoraide Granchi
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
| | - Bart Janssen
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
| | - Graham Hamilton
- Glasgow Polyomics, University of Glasgow, Glasgow G61 1QH, UK;
| | - Hing Y. Leung
- Institute of Cancer Sciences, University of Glasgow, Glasgow G61 1QH, UK;
- CRUK Beatson Institute, Glasgow G61 1BD, UK
- Correspondence: (H.Y.L.); (I.J.B.)
| | - Inès J. Beumer
- GenomeScan B.V. Plesmanlaan 1D, 2333 BZ Leiden, The Netherlands; (M.C.); (M.G.); (Z.G.); (B.J.)
- Correspondence: (H.Y.L.); (I.J.B.)
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38
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Annala M, Fu S, Bacon JVW, Sipola J, Iqbal N, Ferrario C, Ong M, Wadhwa D, Hotte SJ, Lo G, Tran B, Wood LA, Gingerich JR, North SA, Pezaro CJ, Ruether JD, Sridhar SS, Kallio HML, Khalaf DJ, Wong A, Beja K, Schönlau E, Taavitsainen S, Nykter M, Vandekerkhove G, Azad AA, Wyatt AW, Chi KN. Cabazitaxel versus abiraterone or enzalutamide in poor prognosis metastatic castration-resistant prostate cancer: a multicentre, randomised, open-label, phase II trial. Ann Oncol 2021; 32:896-905. [PMID: 33836265 DOI: 10.1016/j.annonc.2021.03.205] [Citation(s) in RCA: 30] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2020] [Revised: 03/10/2021] [Accepted: 03/29/2021] [Indexed: 01/05/2023] Open
Abstract
BACKGROUND Treatment of poor prognosis metastatic castration-resistant prostate cancer (mCRPC) includes taxane chemotherapy and androgen receptor pathway inhibitors (ARPI). We sought to determine optimal treatment in this setting. PATIENTS AND METHODS This multicentre, randomised, open-label, phase II trial recruited patients with ARPI-naive mCRPC and poor prognosis features (presence of liver metastases, progression to mCRPC after <12 months of androgen deprivation therapy, or ≥4 of 6 clinical criteria). Patients were randomly assigned 1 : 1 to receive cabazitaxel plus prednisone (group A) or physician's choice of enzalutamide or abiraterone plus prednisone (group B) at standard doses. Patients could cross over at progression. The primary endpoint was clinical benefit rate for first-line treatment (defined as prostate-specific antigen response ≥50%, radiographic response, or stable disease ≥12 weeks). RESULTS Ninety-five patients were accrued (median follow-up 21.9 months). First-line clinical benefit rate was greater in group A versus group B (80% versus 62%, P = 0.039). Overall survival was not different between groups A and B (median 37.0 versus 15.5 months, hazard ratio (HR) = 0.58, P = 0.073) nor was time to progression (median 5.3 versus 2.8 months, HR = 0.87, P = 0.52). The most common first-line treatment-related grade ≥3 adverse events were neutropenia (cabazitaxel 32% versus ARPI 0%), diarrhoea (9% versus 0%), infection (9% versus 0%), and fatigue (7% versus 5%). Baseline circulating tumour DNA (ctDNA) fraction above the cohort median and on-treatment ctDNA increase were associated with shorter time to progression (HR = 2.38, P < 0.001; HR = 4.03, P < 0.001). Patients with >30% ctDNA fraction at baseline had markedly shorter overall survival than those with undetectable ctDNA (HR = 38.22, P < 0.001). CONCLUSIONS Cabazitaxel was associated with a higher clinical benefit rate in patients with ARPI-naive poor prognosis mCRPC. ctDNA abundance was prognostic independent of clinical features, and holds promise as a stratification biomarker.
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Affiliation(s)
- M Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - S Fu
- Department of Medical Oncology, BC Cancer, Vancouver, Canada; Oncology, School of Medical Sciences, University of Auckland, Auckland, New Zealand
| | - J V W Bacon
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - J Sipola
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - N Iqbal
- Medical Oncology, Saskatoon Cancer Centre, University of Saskatchewan, Saskatoon, Canada
| | - C Ferrario
- Jewish General Hospital, McGill University, Montréal, Quebec, Canada
| | - M Ong
- Department of Medicine, Division of Medical Oncology, The Ottawa Hospital and the University of Ottawa, Ottawa, Canada
| | - D Wadhwa
- BC Cancer - Kelowna Centre, Kelowna, Canada
| | - S J Hotte
- Oncology, Juravinski Cancer Centre, Hamilton, Canada
| | - G Lo
- Department of Medical Oncology, R. S. McLaughlin Durham Regional Cancer Centre, Lakeridge Health, Oshawa, Canada
| | - B Tran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - L A Wood
- QEII Health Sciences Centre, Halifax, Canada
| | - J R Gingerich
- Department of Medical Oncology and Hematology, Cancer Care Manitoba, Winnipeg, Canada
| | - S A North
- Department of Oncology, University of Alberta, Edmonton, Canada
| | - C J Pezaro
- Eastern Health Clinical School, Monash University, Australia; Department of Oncology, Eastern Health, Australia
| | | | - S S Sridhar
- Department of Medical Oncology and Hematology, Princess Margaret Cancer Centre, Toronto, Canada
| | - H M L Kallio
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - D J Khalaf
- Department of Medical Oncology, BC Cancer, Vancouver, Canada
| | - A Wong
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - K Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - E Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - S Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - M Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - G Vandekerkhove
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada
| | - A A Azad
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - A W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Michael Smith Genome Sciences Centre, BC Cancer, Vancouver, Canada.
| | - K N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, Canada; Department of Medical Oncology, BC Cancer, Vancouver, Canada.
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Vandekerkhove G, Lavoie JM, Annala M, Murtha AJ, Sundahl N, Walz S, Sano T, Taavitsainen S, Ritch E, Fazli L, Hurtado-Coll A, Wang G, Nykter M, Black PC, Todenhöfer T, Ost P, Gibb EA, Chi KN, Eigl BJ, Wyatt AW. Plasma ctDNA is a tumor tissue surrogate and enables clinical-genomic stratification of metastatic bladder cancer. Nat Commun 2021; 12:184. [PMID: 33420073 PMCID: PMC7794518 DOI: 10.1038/s41467-020-20493-6] [Citation(s) in RCA: 77] [Impact Index Per Article: 25.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/03/2020] [Accepted: 12/07/2020] [Indexed: 02/08/2023] Open
Abstract
Molecular stratification can improve the management of advanced cancers, but requires relevant tumor samples. Metastatic urothelial carcinoma (mUC) is poised to benefit given a recent expansion of treatment options and its high genomic heterogeneity. We profile minimally-invasive plasma circulating tumor DNA (ctDNA) samples from 104 mUC patients, and compare to same-patient tumor tissue obtained during invasive surgery. Patient ctDNA abundance is independently prognostic for overall survival in patients initiating first-line systemic therapy. Importantly, ctDNA analysis reproduces the somatic driver genome as described from tissue-based cohorts. Furthermore, mutation concordance between ctDNA and matched tumor tissue is 83.4%, enabling benchmarking of proposed clinical biomarkers. While 90% of mutations are identified across serial ctDNA samples, concordance for serial tumor tissue is significantly lower. Overall, our exploratory analysis demonstrates that genomic profiling of ctDNA in mUC is reliable and practical, and mitigates against disease undersampling inherent to studying archival primary tumor foci. We urge the incorporation of cell-free DNA profiling into molecularly-guided clinical trials for mUC.
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Affiliation(s)
- Gillian Vandekerkhove
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | | | - Matti Annala
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Andrew J Murtha
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Nora Sundahl
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Simon Walz
- Department of Urology, University Hospital Tübingen, Tübingen, Germany
| | - Takeshi Sano
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Sinja Taavitsainen
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Elie Ritch
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Ladan Fazli
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Antonio Hurtado-Coll
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Gang Wang
- Department of Pathology and Laboratory Medicine, BC Cancer, Vancouver, BC, Canada
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Centre, Tampere, Finland
| | - Peter C Black
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
| | - Tilman Todenhöfer
- Studienpraxis Urologie, Nuertingen, Germany
- Medical School, Eberhard-Karls-University Tübingen, Tübingen, Germany
| | - Piet Ost
- Department of Radiation Oncology and Experimental Cancer Research, Ghent University Hospital, Ghent, Belgium
| | - Ewan A Gibb
- Decipher Biosciences, Inc., Vancouver, BC, Canada
| | - Kim N Chi
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Bernhard J Eigl
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada.
| | - Alexander W Wyatt
- Department of Urologic Sciences, Vancouver Prostate Centre, University of British Columbia, Vancouver, BC, Canada.
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Dufva O, Pölönen P, Brück O, Keränen MAI, Klievink J, Mehtonen J, Huuhtanen J, Kumar A, Malani D, Siitonen S, Kankainen M, Ghimire B, Lahtela J, Mattila P, Vähä-Koskela M, Wennerberg K, Granberg K, Leivonen SK, Meriranta L, Heckman C, Leppä S, Nykter M, Lohi O, Heinäniemi M, Mustjoki S. Immunogenomic Landscape of Hematological Malignancies. Cancer Cell 2020; 38:380-399.e13. [PMID: 32649887 DOI: 10.1016/j.ccell.2020.06.002] [Citation(s) in RCA: 85] [Impact Index Per Article: 21.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 04/01/2019] [Revised: 03/27/2020] [Accepted: 05/29/2020] [Indexed: 12/15/2022]
Abstract
Understanding factors that shape the immune landscape across hematological malignancies is essential for immunotherapy development. We integrated over 8,000 transcriptomes and 2,000 samples with multilevel genomics of hematological cancers to investigate how immunological features are linked to cancer subtypes, genetic and epigenetic alterations, and patient survival, and validated key findings experimentally. Infiltration of cytotoxic lymphocytes was associated with TP53 and myelodysplasia-related changes in acute myeloid leukemia, and activated B cell-like phenotype and interferon-γ response in lymphoma. CIITA methylation regulating antigen presentation, cancer type-specific immune checkpoints, such as VISTA in myeloid malignancies, and variation in cancer antigen expression further contributed to immune heterogeneity and predicted survival. Our study provides a resource linking immunology with cancer subtypes and genomics in hematological malignancies.
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MESH Headings
- Acute Disease
- Epigenesis, Genetic
- Gene Expression Profiling/methods
- Gene Expression Regulation, Neoplastic
- Genomics/methods
- HLA Antigens/genetics
- Humans
- Immunotherapy/methods
- Leukemia, Myeloid/genetics
- Leukemia, Myeloid/immunology
- Leukemia, Myeloid/therapy
- Lymphocytes, Tumor-Infiltrating/immunology
- Lymphocytes, Tumor-Infiltrating/metabolism
- Lymphoma, Large B-Cell, Diffuse/genetics
- Lymphoma, Large B-Cell, Diffuse/immunology
- Lymphoma, Large B-Cell, Diffuse/therapy
- Multiple Myeloma/genetics
- Multiple Myeloma/immunology
- Multiple Myeloma/therapy
- Mutation
- Tumor Suppressor Protein p53/genetics
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Affiliation(s)
- Olli Dufva
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center (HUH CCC), 00029 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki (UH), 00029 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Petri Pölönen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Oscar Brück
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center (HUH CCC), 00029 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki (UH), 00029 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Mikko A I Keränen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center (HUH CCC), 00029 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki (UH), 00029 Helsinki, Finland
| | - Jay Klievink
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center (HUH CCC), 00029 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki (UH), 00029 Helsinki, Finland
| | - Juha Mehtonen
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland
| | - Jani Huuhtanen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center (HUH CCC), 00029 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki (UH), 00029 Helsinki, Finland
| | - Ashwini Kumar
- Institute for Molecular Medicine Finland, UH, 00014 Helsinki, Finland
| | - Disha Malani
- Institute for Molecular Medicine Finland, UH, 00014 Helsinki, Finland
| | - Sanna Siitonen
- Department of Clinical Chemistry, UH and HUSLAB, HUH, 00029 Helsinki, Finland
| | - Matti Kankainen
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center (HUH CCC), 00029 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki (UH), 00029 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland
| | - Bishwa Ghimire
- Institute for Molecular Medicine Finland, UH, 00014 Helsinki, Finland
| | - Jenni Lahtela
- Institute for Molecular Medicine Finland, UH, 00014 Helsinki, Finland
| | - Pirkko Mattila
- Institute for Molecular Medicine Finland, UH, 00014 Helsinki, Finland
| | | | | | - Kirsi Granberg
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University (TU), 33014 Tampere, Finland
| | - Suvi-Katri Leivonen
- Department of Oncology, HUH CCC, 00029 Helsinki, Finland; Applied Tumor Genomics Research Program, Faculty of Medicine, UH, 00014 Helsinki, Finland
| | - Leo Meriranta
- Department of Oncology, HUH CCC, 00029 Helsinki, Finland; Applied Tumor Genomics Research Program, Faculty of Medicine, UH, 00014 Helsinki, Finland
| | - Caroline Heckman
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland; Institute for Molecular Medicine Finland, UH, 00014 Helsinki, Finland
| | - Sirpa Leppä
- iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland; Department of Oncology, HUH CCC, 00029 Helsinki, Finland; Applied Tumor Genomics Research Program, Faculty of Medicine, UH, 00014 Helsinki, Finland
| | - Matti Nykter
- Laboratory of Computational Biology, Faculty of Medicine and Health Technology, Tampere University (TU), 33014 Tampere, Finland
| | - Olli Lohi
- Tampere Center for Child Health Research, TU and Tays Cancer Center, Tampere University Hospital, 33521 Tampere, Finland
| | - Merja Heinäniemi
- Institute of Biomedicine, School of Medicine, University of Eastern Finland, 70211 Kuopio, Finland.
| | - Satu Mustjoki
- Hematology Research Unit Helsinki, Helsinki University Hospital Comprehensive Cancer Center (HUH CCC), 00029 Helsinki, Finland; Translational Immunology Research Program and Department of Clinical Chemistry and Hematology, University of Helsinki (UH), 00029 Helsinki, Finland; iCAN Digital Precision Cancer Medicine Flagship, Helsinki, Finland.
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Dufva O, Pölönen P, Brück O, Keränen MAI, Klievink J, Mehtonen J, Huuhtanen J, Kumar A, Malani D, Siitonen S, Kankainen M, Ghimire B, Lahtela J, Mattila P, Vähä-Koskela M, Wennerberg K, Granberg K, Leivonen SK, Meriranta L, Heckman C, Leppä S, Nykter M, Lohi O, Heinäniemi M, Mustjoki S. Immunogenomic Landscape of Hematological Malignancies. Cancer Cell 2020; 38:424-428. [PMID: 32931743 DOI: 10.1016/j.ccell.2020.08.019] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Raittinen PVH, Pennanen P, Syvälä H, Bläuer M, Ikonen N, Nätkin R, Nykter M, Tammela T, Ilmonen P, Murtola TT. Abstract 5913: Genetic landscape changes in metastatic prostate cancer after sequential steps of androgen targeted therapy. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-5913] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Metastatic prostate cancer is non-curable fatal disease requiring active treatment. Prostate cancer cell proliferation requires androgen hormones mediated by androgen receptor (AR). Typical metastatic prostate cancer treatment exploits this dependency by systemic androgen deprivation and AR inhibition. While androgen deprivation therapy (ADT) effectively halts cancer cell proliferation, the cells adapt to the limited androgen supply over time by up-regulating AR, making ADT ineffective and creating castration-resistant prostate cancer (CRPC). Androgen receptor signaling inhibitors (ARSIs) such as enzalutamide remain effective even after CRPC development. These drugs have effectively replaced usage of AR inhibitors such as bicalutamide in clinical management of CRPC. However, over time cancer cells undergo further genetic transformations leading to ARSI resistance. Some genetic adaptation mechanisms behind this are known, e.g., AR over-expression and alternative splicing of AR. However, detailed genetic landscape shift is unknown. Moreover, it is unknown whether different AR inhibitors or their sequencing may affect cancer cell genotype and phenotype similarly.
We compare genetic profiles of two different multiresistant VCaP cell populations achieved by long-term cell culture. Two treatment paths are: A. ADT, bicalutamide (BIC), and enzalutamide (ENZA) sequentially; and B. ADT and ENZA sequentially, without bicalutamide. Each consequent treatment is continued as long as it takes for the cells to regain cellular proliferation despite the treatment in order to induce adaptive genetic transformations required for treatment resistance. Once cell proliferation resumes, the obtained resistant cell population is sequenced for mRNA expression levels and splice variant distribution. The genetic profiles of treatment path A and B are compared by analyzing differentially expressed genes and splice variant expression distributions. At the end of the treatment paths, both cell populations are exposed to variable doses of docetaxel to investigate whether ADT- and ARSI-resistant genetic profile affects vulnerability to subsequent chemotherapy.
There was no difference in AR expression or AR splice variant distribution between the treatment paths A and B. AR splicing variants are observed after ARSI resistance. However, multiple other cancer-related genes are differentially expressed between the treatment paths, including FOS, CCND1, IGF1R, and AGR2 which were down-regulated by BIC and heavily up-regulated by ENZA. These genetic alterations also translate into proteomic changes. Remarkably, cells treated with BIC prior to ENZA responded significantly better to docetaxel than ENZA-only treated cells (100 nM dose treatment left 73.75% and 64.55 % cells dead, respectively).
ENZA treatment drives genetic landscape shift in cancer cells when achieving treatment resistance. However, this differs by treatment sequencing; observed genetic transformations differ by whether ENZA treatment was preceded by BIC exposure. Importantly, the differences in the genetic profile lead to greater chemoresistance in cells not treated with BIC before ENZA as compared to cells receiving both treatments. This observation may have implications in optimal sequencing of treatment in CRPC.
Citation Format: Paavo V. H. Raittinen, Pasi Pennanen, Heimo Syvälä, Merja Bläuer, Niina Ikonen, Reetta Nätkin, Matti Nykter, Teuvo Tammela, Pauliina Ilmonen, Teemu T. Murtola. Genetic landscape changes in metastatic prostate cancer after sequential steps of androgen targeted therapy [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr 5913.
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Granberg KJ, Tuominen J, Nordfors K, Pekkarinen M, Kytölä V, Häyrynen S, Afyounian E, Lohi O, Helen P, Kesseli J, Haapasalo J, Haapasalo H, Nykter M. Abstract LB-173: DNA methylation analysis reveals epigenetic regulation of neural differentiation in AT/RTs. Cancer Res 2020. [DOI: 10.1158/1538-7445.am2020-lb-173] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
DNA methylation has proven to be powerful for brain tumor characterization and diagnostic classification. To obtain information about the oncogenic role of DNA methylation, we analyzed medulloblastoma, choroid plexus, and atypical teratoid/rhabdoid tumors (AT/RTs) with public data from 450K-methylation arrays (N=584) and gene-expression arrays (N=110). In addition, two AT/RTs, five choroid plexus tumors and three medulloblastomas were analyzed by using reduced representation bisulfite sequencing, exome sequencing, and RNA-sequencing of matched samples. Only few somatic alterations in addition to SMARCB1 deletion were present in our AT/RTs. DNA methylation analysis generated 2325-5739 and 17175-25187 differentially methylated regions (DMRs) between tumor types in 450K array and RRBS sequencing data, respectively. AT/RTs harbored generally higher DNA methylation levels than the other tumor types. Next, DNA methylation differences were integrated with gene expression data. Surprisingly, only eight genes showed cancer-specific association between differential DNA methylation and an opposite expression change at promoter or linked enhancer in both public and in-house data. There were 44 cancer-specific genes with expression-methylation association when DNA methylation analysis was extended to genomic neighborhoods. To gain information about changes in epigenetic regulation between tumor types, we studied which previously experimentally validated transcription factor (TF) binding sites are enriched in cancer specific DMRs. Several TFs known to promote neural development, such as NEUROG2 and NEUROD1, were enriched in regions hypermethylated in AT/RT, whereas TFs, such as SMAD2, involved in the inhibition of neural development were associated with regions hypermethylated in medulloblastoma. This suggests that DNA methylation is regulating especially the target sites for neural regulators in AT/RT tumors, thus inhibiting neural development. Expression differences did not explain the predicted decreased activity of most of these neural TFs. Low number of genes with cancer-specific expression and methylation change is at least partly explained by the different gene expression patterns in medulloblastomas and choroid plexus tumors, thus providing different references for comparison. Also differences in the measurement techniques contribute to this. Taken together, these results suggest that DNA methylation has a role as an epigenetic regulator for the oncogenesis of AT/RTs.
Citation Format: Kirsi Johanna Granberg, Joonas Tuominen, Kristiina Nordfors, Meeri Pekkarinen, Ville Kytölä, Sergei Häyrynen, Ebrahim Afyounian, Olli Lohi, Pauli Helen, Juha Kesseli, Joonas Haapasalo, Hannu Haapasalo, Matti Nykter. DNA methylation analysis reveals epigenetic regulation of neural differentiation in AT/RTs [abstract]. In: Proceedings of the Annual Meeting of the American Association for Cancer Research 2020; 2020 Apr 27-28 and Jun 22-24. Philadelphia (PA): AACR; Cancer Res 2020;80(16 Suppl):Abstract nr LB-173.
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Affiliation(s)
| | | | | | | | | | | | | | - Olli Lohi
- 2Tampere University Hospital, Tampere, Finland
| | - Pauli Helen
- 2Tampere University Hospital, Tampere, Finland
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Yang M, Petralia F, Li Z, Li H, Ma W, Song X, Kim S, Lee H, Yu H, Lee B, Bae S, Heo E, Kaczmarczyk J, Stępniak P, Warchoł M, Yu T, Calinawan AP, Boutros PC, Payne SH, Reva B, Boja E, Rodriguez H, Stolovitzky G, Guan Y, Kang J, Wang P, Fenyö D, Saez-Rodriguez J, Aderinwale T, Afyounian E, Agrawal P, Ali M, Amadoz A, Azuaje F, Bachman J, Bae S, Bhalla S, Carbonell-Caballero J, Chakraborty P, Chaudhary K, Choi Y, Choi Y, Çubuk C, Dhanda SK, Dopazo J, Elo LL, Fóthi Á, Gevaert O, Granberg K, Greiner R, Heo E, Hidalgo MR, Jayaswal V, Jeon H, Jeon M, Kalmady SV, Kambara Y, Kang J, Kang K, Kaoma T, Kaur H, Kazan H, Kesar D, Kesseli J, Kim D, Kim K, Kim SY, Kim S, Kumar S, Lee B, Lee H, Liu Y, Luethy R, Mahajan S, Mahmoudian M, Muller A, Nazarov PV, Nguyen H, Nykter M, Okuda S, Park S, Pal Singh Raghava G, Rajapakse JC, Rantapero T, Ryu H, Salavert F, Saraei S, Sharma R, Siitonen A, Sokolov A, Subramanian K, Suni V, Suomi T, Tranchevent LC, Usmani SS, Välikangas T, Vega R, Zhong H. Community Assessment of the Predictability of Cancer Protein and Phosphoprotein Levels from Genomics and Transcriptomics. Cell Syst 2020; 11:186-195.e9. [DOI: 10.1016/j.cels.2020.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/22/2019] [Revised: 03/12/2020] [Accepted: 06/29/2020] [Indexed: 10/23/2022]
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45
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Lindfors K, Lin J, Lee HS, Hyöty H, Nykter M, Kurppa K, Liu E, Koletzko S, Rewers M, Hagopian W, Toppari J, Ziegler AG, Akolkar B, Krischer JP, Petrosino JF, Lloyd RE, Agardh D. Metagenomics of the faecal virome indicate a cumulative effect of enterovirus and gluten amount on the risk of coeliac disease autoimmunity in genetically at risk children: the TEDDY study. Gut 2020; 69:1416-1422. [PMID: 31744911 PMCID: PMC7234892 DOI: 10.1136/gutjnl-2019-319809] [Citation(s) in RCA: 59] [Impact Index Per Article: 14.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Revised: 11/01/2019] [Accepted: 11/05/2019] [Indexed: 01/27/2023]
Abstract
OBJECTIVE Higher gluten intake, frequent gastrointestinal infections and adenovirus, enterovirus, rotavirus and reovirus have been proposed as environmental triggers for coeliac disease. However, it is not known whether an interaction exists between the ingested gluten amount and viral exposures in the development of coeliac disease. This study investigated whether distinct viral exposures alone or together with gluten increase the risk of coeliac disease autoimmunity (CDA) in genetically predisposed children. DESIGN The Environmental Determinants of Diabetes in the Young study prospectively followed children carrying the HLA risk haplotypes DQ2 and/or DQ8 and constructed a nested case-control design. From this design, 83 CDA case-control pairs were identified. Median age of CDA was 31 months. Stool samples collected monthly up to the age of 2 years were analysed for virome composition by Illumina next-generation sequencing followed by comprehensive computational virus profiling. RESULTS The cumulative number of stool enteroviral exposures between 1 and 2 years of age was associated with an increased risk for CDA. In addition, there was a significant interaction between cumulative stool enteroviral exposures and gluten consumption. The risk conferred by stool enteroviruses was increased in cases reporting higher gluten intake. CONCLUSIONS Frequent exposure to enterovirus between 1 and 2 years of age was associated with increased risk of CDA. The increased risk conferred by the interaction between enteroviruses and higher gluten intake indicate a cumulative effect of these factors in the development of CDA.
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Affiliation(s)
- Katri Lindfors
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
| | - Jake Lin
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
- Institute for Molecular Medicine Finland, University of Helsinki, Helsinki, Finland
| | - Hye-Seung Lee
- Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Heikki Hyöty
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
| | - Kalle Kurppa
- Faculty of Medicine and Health Techology, Tampere University, Tampere, Finland
- Center for Child Health Research, Tampere University and Tampere University Hospital, Tampere, Finland
- The University Consortium of Seinäjoki, Seinäjoki, Finland
| | - Edwin Liu
- University of Colorado Denver, Anschutz Medical Campus, Aurora, Colorado, USA
- Digestive Health Institute, Children's Hospital Colorado, Aurora, United States
| | - Sibylle Koletzko
- Ludwig-Maximilians-Universitat Munchen, Munchen, Bayern, Germany
- Division of Paediatric Gastroenterology and Hepatology, Dr von Hauner Children's Hospital, Munchen, Germany
| | - Marian Rewers
- Barbara Davis Center for Childhood Diabetes, University of Colorado Denver, Denver, Colorado, USA
| | | | - Jorma Toppari
- Research Centre for Integrative Physiology and Phamacology, Institute of Biomedicine, University of Turku, Turku, Finland
- Department of Paediatrics, Turku University Hospital, Turku, Finland
| | - Annette-Gabriele Ziegler
- Kliikum Rechts der Isar, Technische Universität München, Munchen, Bayern, Germany
- Institute of Diabetes Research, Helmholtz Zentrum München, Germany
- Forschergruppe Diabetes e.V, Neuherberg, Germany
| | - Beena Akolkar
- National Institute of Diabetes and Digestive and Kidney Disease, National Institutes of Health, Bethesda, Maryland, USA
| | - Jeffrey P Krischer
- Morsani College of Medicine, University of South Florida, Tampa, Florida, USA
| | - Joseph F Petrosino
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Richard E Lloyd
- Alkek Center for Metagenomics and Microbiome Research, Department of Molecular Virology and Microbiology, Baylor College of Medicine, Houston, Texas, USA
| | - Daniel Agardh
- The Diabetes and Celiac Disease Unit, Department of Clinical Sciences, Lund University, Lund, Sweden
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Gundem G, Van Loo P, Kremeyer B, Alexandrov LB, Tubio JMC, Papaemmanuil E, Brewer DS, Kallio HML, Hägnäs G, Annala M, Kivinummi K, Goody V, Latimer C, O'Meara S, Dawson KJ, Isaacs W, Emmert-Buck MR, Nykter M, Foster C, Kote-Jarai Z, Easton D, Whitaker HC, Neal DE, Cooper CS, Eeles RA, Visakorpi T, Campbell PJ, McDermott U, Wedge DC, Bova GS. Author Correction: The evolutionary history of lethal metastatic prostate cancer. Nature 2020; 584:E18. [PMID: 32728210 DOI: 10.1038/s41586-020-2581-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
An amendment to this paper has been published and can be accessed via a link at the top of the paper.
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Affiliation(s)
- Gunes Gundem
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Peter Van Loo
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.,Department of Human Genetics, KU Leuven, Herestraat 49 Box 602, B-3000, Leuven, Belgium.,Cancer Research UK London Research Institute, London, WC2A3LY, UK
| | - Barbara Kremeyer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Ludmil B Alexandrov
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Jose M C Tubio
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Elli Papaemmanuil
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Daniel S Brewer
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,The Genome Analysis Centre, Norwich, NR4 7UH, UK
| | - Heini M L Kallio
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Gunilla Hägnäs
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Matti Annala
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Kati Kivinummi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Victoria Goody
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Calli Latimer
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Sarah O'Meara
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Kevin J Dawson
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - William Isaacs
- The James Buchanan Brady Urological Institute, Johns Hopkins School of Medicine, Baltimore, Maryland, 21287, USA
| | - Michael R Emmert-Buck
- Laboratory of Pathology, National Cancer Institute, National Institutes of Health, Maryland, 20892, USA.,Avoneaux Medical Institute, Oxford, Maryland, 21654, USA
| | - Matti Nykter
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Christopher Foster
- University of Liverpool andHCA Pathology Laboratories, London, WC1E6JA, UK
| | - Zsofia Kote-Jarai
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK
| | - Douglas Easton
- Centre for Cancer Genetic Epidemiology, Department of Oncology, University of Cambridge, Cambridge, CB18RN, UK
| | - Hayley C Whitaker
- Uro-oncology Research Group, Cancer ResearchUKCambridge Institute, Cambridge, CB20RE, UK
| | | | - David E Neal
- Uro-oncology Research Group, Cancer ResearchUKCambridge Institute, Cambridge, CB20RE, UK.,Department of Surgical Oncology, University of Cambridge, Addenbrooke's Hospital, Cambridge, CB2 0QQ, UK
| | - Colin S Cooper
- Norwich Medical School and Department of Biological Sciences, University of East Anglia, Norwich, NR4 7TJ, UK.,Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK
| | - Rosalind A Eeles
- Division of Genetics and Epidemiology, The Institute Of Cancer Research, London, SW73RP, UK.,Royal Marsden NHS Foundation Trust, London SW3 6JJ, UK; and, Sutton, SM2 5PT, UK
| | - Tapio Visakorpi
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
| | - Peter J Campbell
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - Ultan McDermott
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK
| | - David C Wedge
- Cancer Genome Project, Wellcome Trust Sanger Institute, Hinxton, CB10 1SA, UK.
| | - G Steven Bova
- Institute of Biosciences and Medical Technology, BioMediTech, University of Tampere and Fimlab Laboratories, Tampere University Hospital, Tampere, FI-33520, Finland
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47
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Kohvakka A, Sattari M, Shcherban A, Annala M, Urbanucci A, Kesseli J, Tammela TLJ, Kivinummi K, Latonen L, Nykter M, Visakorpi T. AR and ERG drive the expression of prostate cancer specific long noncoding RNAs. Oncogene 2020; 39:5241-5251. [PMID: 32555329 DOI: 10.1038/s41388-020-1365-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/06/2020] [Revised: 05/25/2020] [Accepted: 06/08/2020] [Indexed: 01/04/2023]
Abstract
Long noncoding RNAs (lncRNAs) play pivotal roles in cancer development and progression, and some function in a highly cancer-specific manner. However, whether the cause of their expression is an outcome of a specific regulatory mechanism or nonspecific transcription induced by genome reorganization in cancer remains largely unknown. Here, we investigated a group of lncRNAs that we previously identified to be aberrantly expressed in prostate cancer (PC), called TPCATs. Our high-throughput real-time PCR experiments were integrated with publicly available RNA-seq and ChIP-seq data and revealed that the expression of a subset of TPCATs is driven by PC-specific transcription factors (TFs), especially androgen receptor (AR) and ETS-related gene (ERG). Our in vitro validations confirmed that AR and ERG regulated a subset of TPCATs, most notably for EPCART. Knockout of EPCART was found to reduce migration and proliferation of the PC cells in vitro. The high expression of EPCART and two other TPCATs (TPCAT-3-174133 and TPCAT-18-31849) were also associated with the biochemical recurrence of PC in prostatectomy patients and were independent prognostic markers. Our findings suggest that the expression of numerous PC-associated lncRNAs is driven by PC-specific mechanisms and not by random cellular events that occur during cancer development. Furthermore, we report three prospective prognostic markers for the early detection of advanced PC and show EPCART to be a functionally relevant lncRNA in PC.
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Affiliation(s)
- Annika Kohvakka
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Mina Sattari
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Anastasia Shcherban
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Matti Annala
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Alfonso Urbanucci
- Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Juha Kesseli
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Teuvo L J Tammela
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland.,Department of Urology, Tampere University Hospital, Tampere, Finland
| | - Kati Kivinummi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Leena Latonen
- Institute of Biomedicine, University of Eastern Finland, Kuopio, Finland
| | - Matti Nykter
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland
| | - Tapio Visakorpi
- Faculty of Medicine and Health Technology, Tampere University and Tays Cancer Center, Tampere University Hospital, Tampere, Finland. .,Fimlab Laboratories Ltd, Tampere University Hospital, Tampere, Finland.
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48
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Gubina N, Naudi A, Stefanatos R, Jove M, Scialo F, Fernandez-Ayala DJ, Rantapero T, Yurkevych I, Portero-Otin M, Nykter M, Lushchak O, Navas P, Pamplona R, Sanz A. Essential Physiological Differences Characterize Short- and Long-Lived Strains of Drosophila melanogaster. J Gerontol A Biol Sci Med Sci 2020; 74:1835-1843. [PMID: 29945183 DOI: 10.1093/gerona/gly143] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2018] [Indexed: 12/17/2022] Open
Abstract
Aging is a multifactorial process which affects all animals. Aging as a result of damage accumulation is the most accepted explanation but the proximal causes remain to be elucidated. There is also evidence indicating that aging has an important genetic component. Animal species age at different rates and specific signaling pathways, such as insulin/insulin-like growth factor, can regulate life span of individuals within a species by reprogramming cells in response to environmental changes. Here, we use an unbiased approach to identify novel factors that regulate life span in Drosophila melanogaster. We compare the transcriptome and metabolome of two wild-type strains used widely in aging research: short-lived Dahomey and long-lived Oregon R flies. We found that Dahomey flies carry several traits associated with short-lived individuals and species such as increased lipoxidative stress, decreased mitochondrial gene expression, and increased Target of Rapamycin signaling. Dahomey flies also have upregulated octopamine signaling known to stimulate foraging behavior. Accordingly, we present evidence that increased foraging behavior, under laboratory conditions where nutrients are in excess increases damage generation and accelerates aging. In summary, we have identified several new pathways, which influence longevity highlighting the contribution and importance of the genetic component of aging.
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Affiliation(s)
- Nina Gubina
- Institute of Theoretical and Experimental Biophysics, Russian Academy of Sciences, Pushchino, Russia
| | - Alba Naudi
- Department of Experimental Medicine, University of Lleida-IRB, Lleida, Spain
| | - Rhoda Stefanatos
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Mariona Jove
- Department of Experimental Medicine, University of Lleida-IRB, Lleida, Spain
| | - Filippo Scialo
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Daniel J Fernandez-Ayala
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, and CIBERER, ISCIII, Seville, Spain
| | - Tommi Rantapero
- Faculty of Medicine and Life Sciences, BioMediTech Institute, University of Tampere, Finland
| | - Ihor Yurkevych
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Manuel Portero-Otin
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
| | - Matti Nykter
- Faculty of Medicine and Life Sciences, BioMediTech Institute, University of Tampere, Finland
| | - Oleh Lushchak
- Department of Biochemistry and Biotechnology, Vasyl Stefanyk Precarpathian National University, Ivano-Frankivsk, Ukraine
| | - Placido Navas
- Centro Andaluz de Biología del Desarrollo, Universidad Pablo de Olavide-CSIC, and CIBERER, ISCIII, Seville, Spain
| | - Reinald Pamplona
- Department of Experimental Medicine, University of Lleida-IRB, Lleida, Spain
| | - Alberto Sanz
- Institute for Cell and Molecular Biosciences, Newcastle University Institute for Ageing, Newcastle University, Newcastle upon Tyne, UK
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49
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Warner E, Yip S, Annala M, Wang G, Angeles A, Beigi A, Schönlau E, Wong A, Taavitsainen S, Vandekerkhove G, Beja K, Nykter M, Khalaf D, Chi K, Wyatt A. Abstract PR09: Frequency and etiology of ctDNA-positive metastatic prostate cancer with BRCA2, ATM, or CDK12 mutations. Clin Cancer Res 2020. [DOI: 10.1158/1557-3265.liqbiop20-pr09] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Abstract
Recent sequencing efforts have shown that genomic alterations within DNA damage repair (DDR) pathways are relatively common in metastatic prostate cancer (mPCa). Patients harboring DDR gene aberrations can respond poorly to standard-of-care androgen receptor (AR)-targeted therapy, potentially because defective DNA repair enables rapid tumor evolution. Research has shown that DDR-deficient mPCa is often genetically unstable due to its high mutation frequency; however, the specific differences in mutations and copy number alterations between DDR mutant and nonmutant tumors have not been established. We performed targeted next-generation sequencing on 1,214 cell-free DNA samples from 718 patients with mPCa. In 30 patients with disruption of BRCA2, ATM, or CDK12, we also sequenced archival primary tumor tissue. 118 patients had a deleterious germline or somatic mutation in at least one of the 22 DDR genes on our targeted panel. The most commonly altered were BRCA2 (n=41), ATM (n=20), and CDK12 (n=21), together present in ~14% of patients. Disruption of the intact second allele was detected in 96%, 82%, and 84% of patients with mutations in BRCA2, ATM, and CDK12, respectively. Patients with a mutation in any one of these genes had fewer mutations in TP53 than a control cohort of DDR-intact patients (p<0.05). However, BRCA2-defective patients had frequent compound deletions of tumor-suppressor genes (TP53, PTEN, RB1). In patients with CDK12 mutations, PTEN or RB1 deletion was rare and samples instead exhibited copy number gains of MDM2 and/or CCND1. ATM-deficient cases did not demonstrate the same degree of genomic instability as either BRCA2- or CDK12-defective disease. In summary, patients with BRCA2, ATM, or CDK12 gene disruption possess distinct patterns of genomic alterations. These findings might help clarify why some DDR-deficient mPCa cases represent a more aggressive disease subtype with a poor response to AR-targeted therapy.
This abstract is also being presented as Poster A36.
Citation Format: Evan Warner, Steven Yip, Matti Annala, Gang Wang, Arkhjamil Angeles, Arshia Beigi, Elena Schönlau, Amanda Wong, Sinja Taavitsainen, Gillian Vandekerkhove, Kevin Beja, Matti Nykter, Daniel Khalaf, Kim Chi, Alexander Wyatt. Frequency and etiology of ctDNA-positive metastatic prostate cancer with BRCA2, ATM, or CDK12 mutations [abstract]. In: Proceedings of the AACR Special Conference on Advances in Liquid Biopsies; Jan 13-16, 2020; Miami, FL. Philadelphia (PA): AACR; Clin Cancer Res 2020;26(11_Suppl):Abstract nr PR09.
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Affiliation(s)
- Evan Warner
- 1Vancouver Prostate Centre, Vancouver, BC, Canada,
| | - Steven Yip
- 2British Columbia Cancer Agency, Vancouver, BC, Canada,
| | | | - Gang Wang
- 2British Columbia Cancer Agency, Vancouver, BC, Canada,
| | | | - Arshia Beigi
- 4University of British Columbia, Vancouver, BC, Canada
| | | | - Amanda Wong
- 1Vancouver Prostate Centre, Vancouver, BC, Canada,
| | | | | | - Kevin Beja
- 1Vancouver Prostate Centre, Vancouver, BC, Canada,
| | | | - Daniel Khalaf
- 2British Columbia Cancer Agency, Vancouver, BC, Canada,
| | - Kim Chi
- 2British Columbia Cancer Agency, Vancouver, BC, Canada,
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50
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Herberts C, Murtha AJ, Fu S, Wang G, Schönlau E, Xue H, Lin D, Gleave A, Yip S, Angeles A, Hotte S, Tran B, North S, Taavitsainen S, Beja K, Vandekerkhove G, Ritch E, Warner E, Saad F, Iqbal N, Nykter M, Gleave ME, Wang Y, Annala M, Chi KN, Wyatt AW. Activating AKT1 and PIK3CA Mutations in Metastatic Castration-Resistant Prostate Cancer. Eur Urol 2020; 78:834-844. [PMID: 32451180 DOI: 10.1016/j.eururo.2020.04.058] [Citation(s) in RCA: 43] [Impact Index Per Article: 10.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/20/2020] [Accepted: 04/21/2020] [Indexed: 12/18/2022]
Abstract
BACKGROUND Activating mutations in AKT1 and PIK3CA are undercharacterised in metastatic castration-resistant prostate cancer (mCRPC), but are linked to activation of phosphatidylinositol 3-kinase (PI3K) signalling and sensitivity to pathway inhibitors in other cancers. OBJECTIVE To determine the prevalence, genomic context, and clinical associations of AKT1/PIK3CA activating mutations in mCRPC. DESIGN, SETTING, AND PARTICIPANTS We analysed targeted cell-free DNA (cfDNA) sequencing data from 599 metastatic prostate cancer patients with circulating tumour DNA (ctDNA) content above 2%. OUTCOME MEASUREMENTS AND STATISTICAL ANALYSIS In patients with AKT1/PIK3CA mutations, cfDNA was subjected to PTEN intron sequencing and matched diagnostic tumour tissue was analysed when possible. RESULTS AND LIMITATIONS Of the patients, 6.0% (36/599) harboured somatic clonal activating mutation(s) in AKT1 or PIK3CA. Mutant allele-specific imbalance was common. Clonal mutations in mCRPC ctDNA were typically detected in pretreatment primary tissue and were consistent across serial ctDNA collections. AKT1/PIK3CA-mutant mCRPC had fewer androgen receptor (AR) gene copies than AKT1/PIK3CA wild-type mCRPC (median 4.7 vs 10.3, p = 0.003). AKT1 mutations were mutually exclusive with PTEN alterations. Patients with and without AKT1/PIK3CA mutations showed similar clinical outcomes with standard of care treatments. A heavily pretreated mCRPC patient with an AKT1 mutation experienced a 50% decline in prostate-specific antigen with Akt inhibitor (ipatasertib) monotherapy. Ipatasertib also had a marked antitumour effect in a patient-derived xenograft harbouring an AKT1 mutation. Limitations include the inability to assess AKT1/PIK3CA correlatives in ctDNA-negative patients. CONCLUSIONS AKT1/PIK3CA activating mutations are relatively common and delineate a distinct mCRPC molecular subtype with low-level AR copy gain. Clonal prevalence and evidence of mutant allele selection propose PI3K pathway dependency in selected patients. The use of cfDNA screening enables prospective clinical trials to test PI3K pathway inhibitors in this population. PATIENT SUMMARY Of advanced prostate cancer cases, 6% have activating mutations in the genes AKT1 or PIK3CA. These mutations can be identified using a blood test and may help select patients suitable for clinical trials of phosphatidylinositol 3-kinase inhibitors.
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Affiliation(s)
- Cameron Herberts
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Andrew J Murtha
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Simon Fu
- Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada
| | - Gang Wang
- Department of Pathology, BC Cancer, Vancouver, BC, Canada
| | - Elena Schönlau
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Hui Xue
- Department of Experimental Therapeutics, BC Cancer, Vancouver, BC, Canada
| | - Dong Lin
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer, Vancouver, BC, Canada
| | - Anna Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Steven Yip
- Tom Baker Cancer Centre, University of Calgary, Calgary, AB, Canada
| | | | | | - Ben Tran
- Department of Medical Oncology, Peter MacCallum Cancer Centre, Melbourne, Australia
| | - Scott North
- Cross Cancer Institute, Edmonton, AB, Canada
| | | | - Kevin Beja
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Gillian Vandekerkhove
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Elie Ritch
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Evan Warner
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Fred Saad
- Urology, Hospital St. Luc du CHUM, Montreal, QC, Canada
| | - Nayyer Iqbal
- Medical Oncology, Saskatoon Cancer Centre, University of Saskatchewan, Saskatoon, SK, Canada
| | - Matti Nykter
- Institute of Biosciences and Medical Technology, Tampere, Finland
| | - Martin E Gleave
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada
| | - Yuzhuo Wang
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Experimental Therapeutics, BC Cancer, Vancouver, BC, Canada
| | - Matti Annala
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Institute of Biosciences and Medical Technology, Tampere, Finland
| | - Kim N Chi
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada; Department of Medical Oncology, BC Cancer, Vancouver, BC, Canada.
| | - Alexander W Wyatt
- Vancouver Prostate Centre, Department of Urologic Sciences, University of British Columbia, Vancouver, BC, Canada.
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