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Kuusanmäki H, Kytölä S, Vänttinen I, Ruokoranta T, Ranta A, Huuhtanen J, Suvela M, Parsons A, Holopainen A, Partanen A, Kuusisto MEL, Koskela S, Räty R, Itälä-Remes M, Västrik I, Dufva O, Siitonen S, Porkka K, Wennerberg K, Heckman CA, Ettala P, Pyörälä M, Rimpiläinen J, Siitonen T, Kontro M. Ex vivo venetoclax sensitivity testing predicts treatment response in acute myeloid leukemia. Haematologica 2023; 108:1768-1781. [PMID: 36519325 PMCID: PMC10316276 DOI: 10.3324/haematol.2022.281692] [Citation(s) in RCA: 8] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/30/2022] [Accepted: 11/28/2022] [Indexed: 07/25/2023] Open
Abstract
The BCL-2 inhibitor venetoclax has revolutionized the treatment of acute myeloid leukemia (AML) in patients not benefiting from intensive chemotherapy. Nevertheless, treatment failure remains a challenge, and predictive markers are needed, particularly for relapsed or refractory AML. Ex vivo drug sensitivity testing may correlate with outcomes, but its prospective predictive value remains unexplored. Here we report the results of the first stage of the prospective phase II VenEx trial evaluating the utility and predictiveness of venetoclax sensitivity testing using different cell culture conditions and cell viability assays in patients receiving venetoclax-azacitidine. Participants with de novo AML ineligible for intensive chemotherapy, relapsed or refractory AML, or secondary AML were included. The primary endpoint was the treatment response in participants showing ex vivo sensitivity and the key secondary endpoints were the correlation of sensitivity with responses and survival. Venetoclax sensitivity testing was successful in 38/39 participants. Experimental conditions significantly influenced the predictive accuracy. Blast-specific venetoclax sensitivity measured in conditioned medium most accurately correlated with treatment outcomes; 88% of sensitive participants achieved a treatment response. The median survival was significantly longer for participants who were ex vivo-sensitive to venetoclax (14.6 months for venetoclax-sensitive patients vs. 3.5 for venetoclax-insensitive patients, P<0.001). This analysis illustrates the feasibility of integrating drug-response profiling into clinical practice and demonstrates excellent predictivity. This trial is registered with ClinicalTrials.gov identifier: NCT04267081.
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Affiliation(s)
- Heikki Kuusanmäki
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen, Denmark; Foundation for the Finnish Cancer Institute, Helsinki
| | - Sari Kytölä
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | - Ida Vänttinen
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Tanja Ruokoranta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Amanda Ranta
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Jani Huuhtanen
- Hematology Research Unit, University of Helsinki, Helsinki
| | - Minna Suvela
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Alun Parsons
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | | | - Anu Partanen
- Department of Medicine, Kuopio University Hospital, Kuopio
| | - Milla E L Kuusisto
- Department of Medicine, Oulu University Hospital, Oulu, Finland; Department of Hematology, University of Oulu, Oulu
| | - Sirpa Koskela
- Department of Internal Medicine, Tampere University Hospital, Tampere
| | - Riikka Räty
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki
| | | | - Imre Västrik
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Olli Dufva
- Hematology Research Unit, University of Helsinki, Helsinki
| | - Sanna Siitonen
- Department of Clinical Chemistry, University of Helsinki and Helsinki University Hospital
| | - Kimmo Porkka
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki, Finland; Hematology Research Unit, University of Helsinki, Helsinki
| | - Krister Wennerberg
- Biotech Research and Innovation Centre (BRIC), University of Copenhagen, Copenhagen
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki
| | - Pia Ettala
- Department of Clinical Hematology, Turku University Hospital, Turku
| | - Marja Pyörälä
- Department of Medicine, Kuopio University Hospital, Kuopio
| | | | - Timo Siitonen
- Department of Medicine, Oulu University Hospital, Oulu
| | - Mika Kontro
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, Finland; Foundation for the Finnish Cancer Institute, Helsinki, Finland; Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, Helsinki.
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2
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Liu M, Wang Y, Miettinen JJ, Kumari R, Majumder MM, Tierney C, Bazou D, Parsons A, Suvela M, Lievonen J, Silvennoinen R, Anttila P, Dowling P, O'Gorman P, Tang J, Heckman CA. S100 Calcium Binding Protein Family Members Associate With Poor Patient Outcome and Response to Proteasome Inhibition in Multiple Myeloma. Front Cell Dev Biol 2021; 9:723016. [PMID: 34485305 PMCID: PMC8415228 DOI: 10.3389/fcell.2021.723016] [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] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/26/2021] [Indexed: 11/13/2022] Open
Abstract
Despite several new therapeutic options, multiple myeloma (MM) patients experience multiple relapses and inevitably become refractory to treatment. Insights into drug resistance mechanisms may lead to the development of novel treatment strategies. The S100 family is comprised of 21 calcium binding protein members with 17 S100 genes located in the 1q21 region, which is commonly amplified in MM. Dysregulated expression of S100 family members is associated with tumor initiation, progression and inflammation. However, the relationship between the S100 family and MM pathogenesis and drug response is unknown. In this study, the roles of S100 members were systematically studied at the copy number, transcriptional and protein level with patients’ survival and drug response. Copy number analysis revealed a predominant pattern of gains occurring in S100 genes clustering in the 1q21 locus. In general, gains of genes encoding S100 family members associated with worse patient survival. However, S100 gene copy number and S100 gene expression did not necessarily correlate, and high expression of S100A4 associated with poor patient survival. Furthermore, integrated analysis of S100 gene expression and ex vivo drug sensitivity data showed significant negative correlation between expression of S100 family members (S100A8, S100A9, and S100A12) and sensitivity to some drugs used in current MM treatment, including proteasome inhibitors (bortezomib, carfilzomib, and ixazomib) and histone deacetylase inhibitor panobinostat. Combined proteomic and pharmacological data exhibited significant negative association of S100 members (S100A4, S100A8, and S100A9) with proteasome inhibitors and panobinostat. Clinically, the higher expression of S100A4 and S100A10 were significantly linked to shorter progression free survival in patients receiving carfilzomib-based therapy. The results indicate an association and highlight the potential functional importance of S100 members on chromosome 1q21 in the development of MM and resistance to established myeloma drugs, including proteasome inhibitors.
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Affiliation(s)
- Minxia Liu
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Yinyin Wang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Juho J Miettinen
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Romika Kumari
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Muntasir Mamun Majumder
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Ciara Tierney
- Department of Hematology, Mater Misericordiae University Hospital, Dublin, Ireland.,Department of Biology, National University of Ireland, Maynooth, Ireland
| | - Despina Bazou
- Department of Hematology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Alun Parsons
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Minna Suvela
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
| | - Juha Lievonen
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Raija Silvennoinen
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Pekka Anttila
- Department of Hematology, Helsinki University Hospital Comprehensive Cancer Center, University of Helsinki, Helsinki, Finland
| | - Paul Dowling
- Department of Biology, National University of Ireland, Maynooth, Ireland
| | - Peter O'Gorman
- Department of Hematology, Mater Misericordiae University Hospital, Dublin, Ireland
| | - Jing Tang
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Caroline A Heckman
- Institute for Molecular Medicine Finland - FIMM, HiLIFE - Helsinki Institute of Life Science, iCAN Digital Cancer Medicine Flagship, University of Helsinki, Helsinki, Finland
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3
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Malani D, Kumar A, Yadav B, Kontro M, Potdar S, Bruck O, Kytölä S, Saarela J, Eldfors S, Karjalainen R, Majumder MM, Västrik I, Ellonen P, Kankainen M, Suvela M, Knappila S, Parson A, Palva A, Mattila P, Kulesskiy E, Turunen L, Laamanen K, Lehtinen E, Nurmi M, Suomi K, Muruimägi A, Gjertsen BT, Mustjoki S, Anders S, Wolf M, Aittokallio T, Wennerberg K, Heckman C, Porkka K, Kallioniemi O. Abstract 458: Precision systems medicine in acute myeloid leukemia: real-time translation of tailored therapeutic opportunities arising from ex-vivo drug sensitivity testing and molecular profiling. Cancer Res 2019. [DOI: 10.1158/1538-7445.am2019-458] [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
Acute myeloid leukemia (AML) is an aggressive disease of clonal hematopoietic progenitor cells. Here, we applied ex-vivo drug sensitivity and resistance testing on AML patient cells with 362 emerging and 153 approved cancer drugs together with genomic and transcriptomic profiling to identify and tailor therapies for patients with advanced disease. Ex-vivo testing with freshly isolated patient cells revealed cancer-specific efficacies of approved drugs in 97% of the 164 patient cases, including 47% of the cases with no actionable driver mutations. We identified 142 statistically significant associations between drug responses and somatic mutations, including increased sensitivity to JAK inhibitors in patients with NPM1 mutations. Transcriptomic profiles predicted drug responses better than genomics and helped to identify additional response markers, especially beyond mutations. For example, overexpression of HOX family genes was associated with sensitivity to JAK inhibitors in patients with NPM1 mutation. In a prospective study, we translated the functional drug response and molecular profile data to the clinic and suggested tailored therapy with targeted drugs for 26 relapsed or refractory AML patients. In an observational intervention study, acting on these recommendations resulted in a temporary complete clinical remission or leukemia-free state in 39% of the cases. In summary, we conclude that ex-vivo testing of drugs on patient AML cells i) revealed clinically actionable drug efficacies in almost all AML patients, including patients with no actionable mutations, ii) predicted cases with actionable driver mutations with no pharmacological dependency on the target, and iii) enabled real-time tailoring of therapy with 39% clinical response rate in chemorefractory advanced AML. Taken together, we believe this real-time systems medicine approach could become a powerful strategy for tailoring therapies for individual patients in the future.
Citation Format: Disha Malani, Ashwni Kumar, Bhagwan Yadav, Mika Kontro, Swapnil Potdar, Oscar Bruck, Säri Kytölä, Jani Saarela, Samuli Eldfors, Riikka Karjalainen, Muntasir M. Majumder, Imre Västrik, Pekka Ellonen, Matti Kankainen, Minna Suvela, Siv Knappila, Alun Parson, Aino Palva, Pirkko Mattila, Evgeny Kulesskiy, Laura Turunen, Karoliina Laamanen, Elina Lehtinen, Maria Nurmi, Katja Suomi, Astrid Muruimägi, Bjorn T. Gjertsen, Satu Mustjoki, Simon Anders, Maija Wolf, Tero Aittokallio, Krister Wennerberg, Caroline Heckman, Kimmo Porkka, Olli Kallioniemi. Precision systems medicine in acute myeloid leukemia: real-time translation of tailored therapeutic opportunities arising from ex-vivo drug sensitivity testing and molecular profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2019; 2019 Mar 29-Apr 3; Atlanta, GA. Philadelphia (PA): AACR; Cancer Res 2019;79(13 Suppl):Abstract nr 458.
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Affiliation(s)
- Disha Malani
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Ashwni Kumar
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Bhagwan Yadav
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Mika Kontro
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Swapnil Potdar
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Oscar Bruck
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Säri Kytölä
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Jani Saarela
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Samuli Eldfors
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | | | - Imre Västrik
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Pekka Ellonen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Matti Kankainen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Minna Suvela
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Siv Knappila
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Alun Parson
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Aino Palva
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Pirkko Mattila
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | - Laura Turunen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | - Elina Lehtinen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Maria Nurmi
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Katja Suomi
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | | | - Satu Mustjoki
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Simon Anders
- 4Center for Molecular Biology of University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Maija Wolf
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | | | | | - Kimmo Porkka
- 2Hematology Research Unit Helsinki, Helsinki, Finland
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4
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Malani D, Kumar A, Yadav B, Kontro M, Potdar S, Brück O, Kytölä S, Saarela J, Eldfors S, Ojamies P, Riikka K, Majumder MM, Västrik I, Ellonen P, Kankainen M, Suvela M, Knappila S, Parson A, Palva A, Mattila P, Kulesskiy1 E, Turunen L, Laamanen K, Lehtinen E, Mikkonen P, Nurmi M, Timonen S, Murumägi A, Gjersten BT, Mustjoki S, Aittokallio T, Wennerberg K, Anders S, Wolf M, Heckman C, Porkka K, Kallioniemi O. Abstract 3899: Discovery and clinical implementation of individualized therapies in acute myeloid leukemia based on ex vivo drug sensitivity testing and multi-omics profiling. Cancer Res 2018. [DOI: 10.1158/1538-7445.am2018-3899] [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
Acute myeloid leukemia (AML) is a heterogeneous disease characterized by multiple molecular subtypes and lack of effective targeted therapies. Here, we performed extensive molecular profiling and ex vivo drug testing with 515 approved and emerging cancer drugs on 164 AML patient samples. The aim was to i) assign individualized treatment options to advanced AML patients in real time, ii) explore drug response patterns across the molecular subtypes of AML and iii) identify opportunities to repurpose existing and emerging cancer drugs.
Bone marrow samples (n=164) from 129 consecutive AML patients and 17 healthy donors were studied from the Helsinki University Hospital and the Haukeland University Hospital, Bergen. Mononuclear cells were resuspended either in mononuclear cell medium (MCM) or stroma conditioned medium (CM) and tested for drug sensitivity and resistance as previously described (PMID: 24056683) and studied by exome and transcriptome sequencing. The study protocol allowed us to return data to the clinician for consideration of novel treatment options. For the meta-analysis of associations between drug responses and molecular and clinical parameters, Wilcoxon signed ranked test and logistic regression were applied.
Clustering of all patient samples based on ex vivo drug response patterns in both media types identified 7 distinct functional groups of AML. For example, a subgroup of samples was highly resistant to chemotherapeutics and all targeted drugs except BCL-2 inhibitors. The differences in drug responses in the two media types highlighted the importance of assay conditions for ex vivo drug testing. Strong clustering of several drugs in the same drug classes was often observed as well as clustering across different classes, for example between BET (JQ1, I-BET151, birabresib) and MEK (trametinib, cobimetinib) inhibitors. About 24 percent of the FLT3 negative AML patients manifested strong ex vivo sensitivity to glucocorticoids, highlighting a potential drug repositioning opportunity in this subset of AML patients. Overall, we identified 320 significant associations between drugs and mutated driver genes including association between NPM1 mutation and sensitivity to JAK inhibitors.
Altogether, targeted treatment opportunities were clinically tested in 25 occasions in chemorefractory AML patients. The tailored clinical therapy led to transient complete remission or leukemia free state in 36% (9/25) of these cases.
In conclusion, we discovered and clinically implemented individualized therapeutic options for AML patients, which resulted in a 36% clinical responses in a non-randomized proof-of-concept study. The associations identified between ex-vivo drug response and driver mutations provided novel drug repositioning opportunities in specific molecular subtypes.
Citation Format: Disha Malani, Ashwini Kumar, Bhagwan Yadav, Mika Kontro, Swapnil Potdar, Oscar Brück, Sari Kytölä, Jani Saarela, Samuli Eldfors, Poojitha Ojamies, Karjalainen Riikka, Muntasir Mamun Majumder, Imre Västrik, Pekka Ellonen, Matti Kankainen, Minna Suvela, Siv Knappila, Alun Parson, Aino Palva, Pirkko Mattila, Evgeny Kulesskiy1, Laura Turunen, Karoliina Laamanen, Elina Lehtinen, Piia Mikkonen, Maria Nurmi, Sanna Timonen, Astrid Murumägi, Bjorn Tore Gjersten, Satu Mustjoki, Tero Aittokallio, Krister Wennerberg, Simon Anders, Maija Wolf, Caroline Heckman, Kimmo Porkka, Olli Kallioniemi. Discovery and clinical implementation of individualized therapies in acute myeloid leukemia based on ex vivo drug sensitivity testing and multi-omics profiling [abstract]. In: Proceedings of the American Association for Cancer Research Annual Meeting 2018; 2018 Apr 14-18; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2018;78(13 Suppl):Abstract nr 3899.
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Affiliation(s)
- Disha Malani
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Ashwini Kumar
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Bhagwan Yadav
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Mika Kontro
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Swapnil Potdar
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Oscar Brück
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Sari Kytölä
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | - Jani Saarela
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Samuli Eldfors
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | | | | | - Imre Västrik
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Pekka Ellonen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Matti Kankainen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Minna Suvela
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Siv Knappila
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Alun Parson
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Aino Palva
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Pirkko Mattila
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | - Laura Turunen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | - Elina Lehtinen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Piia Mikkonen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Maria Nurmi
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Sanna Timonen
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | - Astrid Murumägi
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | - Satu Mustjoki
- 2Hematology Research Unit Helsinki, Helsinki, Finland
| | | | | | - Simon Anders
- 4Center for Molecular Biology of University of Heidelberg (ZMBH), Heidelberg, Germany
| | - Maija Wolf
- 1Inst. for Molec. Medicine Finland (FIMM), Helsinki, Finland
| | | | - Kimmo Porkka
- 2Hematology Research Unit Helsinki, Helsinki, Finland
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5
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Pemovska T, Kontro M, Yadav B, Edgren H, Eldfors S, Szwajda A, Almusa H, Bespalov MM, Ellonen P, Elonen E, Gjertsen BT, Karjalainen R, Kulesskiy E, Lagström S, Lehto A, Lepistö M, Lundán T, Majumder MM, Marti JML, Mattila P, Murumägi A, Mustjoki S, Palva A, Parsons A, Pirttinen T, Rämet ME, Suvela M, Turunen L, Västrik I, Wolf M, Knowles J, Aittokallio T, Heckman CA, Porkka K, Kallioniemi O, Wennerberg K. Individualized systems medicine strategy to tailor treatments for patients with chemorefractory acute myeloid leukemia. Cancer Discov 2013; 3:1416-29. [PMID: 24056683 DOI: 10.1158/2159-8290.cd-13-0350] [Citation(s) in RCA: 280] [Impact Index Per Article: 25.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
UNLABELLED We present an individualized systems medicine (ISM) approach to optimize cancer drug therapies one patient at a time. ISM is based on (i) molecular profiling and ex vivo drug sensitivity and resistance testing (DSRT) of patients' cancer cells to 187 oncology drugs, (ii) clinical implementation of therapies predicted to be effective, and (iii) studying consecutive samples from the treated patients to understand the basis of resistance. Here, application of ISM to 28 samples from patients with acute myeloid leukemia (AML) uncovered five major taxonomic drug-response subtypes based on DSRT profiles, some with distinct genomic features (e.g., MLL gene fusions in subgroup IV and FLT3-ITD mutations in subgroup V). Therapy based on DSRT resulted in several clinical responses. After progression under DSRT-guided therapies, AML cells displayed significant clonal evolution and novel genomic changes potentially explaining resistance, whereas ex vivo DSRT data showed resistance to the clinically applied drugs and new vulnerabilities to previously ineffective drugs. SIGNIFICANCE Here, we demonstrate an ISM strategy to optimize safe and effective personalized cancer therapies for individual patients as well as to understand and predict disease evolution and the next line of therapy. This approach could facilitate systematic drug repositioning of approved targeted drugs as well as help to prioritize and de-risk emerging drugs for clinical testing.
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Affiliation(s)
- Tea Pemovska
- 1Institute for Molecular Medicine Finland, FIMM; 2Hematology Research Unit Helsinki, Helsinki University Central Hospital, University of Helsinki, Helsinki; 3Department of Clinical Chemistry and TYKSLAB, Turku University Central Hospital, University of Turku, Turku; 4Department of Internal Medicine, Tampere University Hospital, Tampere, Finland; 5Department of Clinical Science, Hematology Section, University of Bergen; and 6Department of Internal Medicine, Hematology Section, Haukeland University Hospital, Bergen, Norway
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6
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Karjalainen R, Eldfors S, Edgren H, Venkata NPK, Kontro M, Majumder MM, Murumägi A, Parsons A, Almusa H, Ellonen P, Lepistö M, Mattila P, Hannula S, Lagström S, Suvela M, Wolf M, Wennerberg K, Knowles JKC, Mustjoki S, Saarela J, Porkka K, Kallioniemi O, Heckman CA. Abstract 5067: Exome sequencing reveals both DNA sequence and copy number changes in AML: Potential driver changes and mechanisms of drug resistance revealed from serial samples from the same patients. Cancer Res 2012. [DOI: 10.1158/1538-7445.am2012-5067] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [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
Despite significant advances in characterizing the molecular genetics of AML, the clonal evolution of leukemic cells and the dynamic impact of genomic changes on the development of the disease and progression to drug resistance are not well understood. Here, we applied next-generation sequencing to quantify aberrant tumor subclones carrying specific mutant alleles of key cancer genes and developed a method to extract quantitative high-resolution copy number changes across the genome using exome sequencing data from matching cancer and normal DNA. Serial bone marrow (BM) samples collected from diagnosis to relapse to post-treatment drug resistance in a patient-centric manner made it possible to trace the clonal evolution of AML and to identify variants potentially involved in drug resistance. Exome sequencing from AML blast cells and normal skin biopsies was performed as part of the Finnish Hematology Registry and Biobanking (FHRB) effort. Consecutive paired samples from different patients revealed unique genetic patterns of clonal evolution and cancer progression in each patient. In a pre-resistant sample of one AML M5 patient, we identified four closely spaced insertions in the Wilm's Tumor (WT1) suppressor gene, none of which appear on the same sequence reads. This suggests the presence of multiple distinct leukemic subclones even before treatment resistance and underscores the strong selective advantage conferred by WT1 mutations. After relapse, one of the subclones was lost, and another one significantly increased suggesting that the relapse arose from the expansion of a pre-existing resistant subclone. In this patient, recurrent clones otherwise featured similar copy number changes and the same fusion genes as the primary diagnostic sample. In another AML patient developing recurrence an opposite pattern was observed: The relapsed, drug-resistant cells displayed an enormous increase of small microdeletions compared to the diagnostic, pre-treatment sample, while almost all sequence-level alterations in potential cancer genes were the same between the two samples. This suggests that a distinct type of DNA repair deficiency may have contributed to the drug resistant clone in this patient. Conclusions: Exome sequencing from paired samples of AML cells before and after relapse makes it possible to trace the clonal evolution of the disease and study the impact of therapy both at the level of sequence alterations of key cancer genes and simultaneously at the level of copy number changes inferred from exome sequence data. This analysis has highlighted multiple genomic patterns by which resistance may evolve in vivo during cancer treatment. Refined bioinformatic analysis and interpretation of exome-seq data provides a rich resource to identify genetic biomarkers of drug response and minimal residual disease.
Citation Format: {Authors}. {Abstract title} [abstract]. In: Proceedings of the 103rd Annual Meeting of the American Association for Cancer Research; 2012 Mar 31-Apr 4; Chicago, IL. Philadelphia (PA): AACR; Cancer Res 2012;72(8 Suppl):Abstract nr 5067. doi:1538-7445.AM2012-5067
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Affiliation(s)
| | - Samuli Eldfors
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Henrik Edgren
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | | | - Mika Kontro
- 2Hematology Research Unit, Department of Medicine, Division of Hematology, Helsinki University Central Hospital, Helsinki, Finland
| | | | | | - Alun Parsons
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Henrikki Almusa
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Pekka Ellonen
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Maija Lepistö
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Pirkko Mattila
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Sari Hannula
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Sonja Lagström
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Minna Suvela
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Maija Wolf
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | | | | | - Satu Mustjoki
- 2Hematology Research Unit, Department of Medicine, Division of Hematology, Helsinki University Central Hospital, Helsinki, Finland
| | - Janna Saarela
- 1Institute for Molecular Medicine Finland, Helsinki, Finland
| | - Kimmo Porkka
- 2Hematology Research Unit, Department of Medicine, Division of Hematology, Helsinki University Central Hospital, Helsinki, Finland
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Kallio SP, Jakkula E, Purcell S, Suvela M, Koivisto K, Tienari PJ, Elovaara I, Pirttilä T, Reunanen M, Bronnikov D, Viander M, Meri S, Hillert J, Lundmark F, Harbo HF, Lorentzen AR, De Jager PL, Daly MJ, Hafler DA, Palotie A, Peltonen L, Saarela J. Use of a genetic isolate to identify rare disease variants: C7 on 5p associated with MS. Hum Mol Genet 2009; 18:1670-83. [PMID: 19221116 DOI: 10.1093/hmg/ddp073] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Large case-control genome-wide association studies primarily expose common variants contributing to disease pathogenesis with modest effects. Thus, alternative strategies are needed to tackle rare, possibly more penetrant alleles. One strategy is to use special populations with a founder effect and isolation, resulting in allelic enrichment. For multiple sclerosis such a unique setting is reported in Southern Ostrobothnia in Finland, where the prevalence and familial occurrence of multiple sclerosis (MS) are exceptionally high. Here, we have studied one of the best replicated MS loci, 5p, and monitored for haplotypes shared among 72 regional MS cases, the majority of which are genealogically distantly related. The haplotype analysis over the 45 Mb region, covering the linkage peak identified in Finnish MS families, revealed only modest association at IL7R (P = 0.04), recently implicated in MS, whereas most significant association was found with one haplotype covering the C7-FLJ40243 locus (P = 0.0001), 5.1 Mb centromeric of IL7R. The finding was validated in an independent sample from the isolate and resulted in an odds ratio of 2.73 (P = 0.000003) in the combined data set. The identified relatively rare risk haplotype contains C7 (complement component 7), an important player of the innate immune system. Suggestive association with alleles of the region was seen also in more heterogeneous populations. Interestingly, also the complement activity correlated with the identified risk haplotype. These results suggest that the MS predisposing locus on 5p is more complex than assumed and exemplify power of population isolates in the identification of rare disease alleles.
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Affiliation(s)
- Suvi P Kallio
- Finnish Institute for Molecular Medicine, Biomedicum, Helsinki, Finland
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Sulonen AM, Kallio SP, Ellonen P, Suvela M, Elovaara I, Koivisto K, Pirttilä T, Reunanen M, Tienari PJ, Palotie A, Peltonen L, Saarela J. No evidence for shared etiology in two demyelinative disorders, MS and PLOSL. J Neuroimmunol 2008; 206:86-90. [PMID: 19019460 DOI: 10.1016/j.jneuroim.2008.10.005] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [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: 06/18/2008] [Revised: 10/08/2008] [Accepted: 10/13/2008] [Indexed: 01/08/2023]
Abstract
Loss-of-function mutations of DAP12 and TREM2 cause a recessively inherited disease PLOSL, manifesting in brain white matter. The genes of the DAP12-TREM2 signaling receptor are located on 19q13.12 and 6p21.1, to which linkage has been observed also in families affected by another immune-mediated demyelinating disease, MS. We have tested if allelic variation in DAP12 or TREM2 predisposes also to MS by monitoring carrier frequency of the Finnish PLOSL mutation in Finnish MS cases and by studying DAP12 and TREM2 in MS by linkage and association. To conclude, the DAP12-TREM2 complex unlikely has a role in genetic susceptibility of MS.
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Affiliation(s)
- Anna-Maija Sulonen
- Finnish Institute for Molecular Medicine, FIMM, and National Public Health Institute, Biomedicum, Helsinki, Finland
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Kanerva M, Jääskeläinen AJ, Suvela M, Piiparinen H, Vaheri A, Pitkäranta A. Human herpesvirus-6 and -7 DNA in cerebrospinal fluid of facial palsy patients. Acta Otolaryngol 2008; 128:460-4. [PMID: 18368583 DOI: 10.1080/00016480701774990] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
Abstract
CONCLUSIONS Finding human herpesvirus (HHV)-7 and dual HHV-6A and -6B DNA in cerebrospinal fluid (CSF) of two facial palsy (FP) patients is intriguing but does not allow etiologic conclusions as such. HHV-6 or -7 DNA was revealed in 10% of the CSF samples tested from 70 immunocompetent adolescents and adults; a highly unusual result. How these findings are associated with the diseases they accompany remains to be defined. OBJECTIVE To determine whether herpes simplex virus (HSV)-1 and -2, varicella-zoster virus (VZV), HHV-6A, -6B, and -7, Epstein-Barr virus (EBV), and cytomegalovirus (CMV) DNA could be found in CSF of FP patients or controls. SUBJECTS AND METHODS In all, 33 peripheral FP patients (26 idiopathic, 5 with herpesvirus infection, 1 puerperal, 1 Melkersson-Rosenthal syndrome) (34 CSF samples) and 36 controls (16 nonidiopathic FP, 7 hearing loss, 6 vertigo, 5 headache, 2 other) previously tested for HSV-1, VZV, and HHV-6 DNA by polymerase chain reaction (PCR) were tested with highly sensitive multiplex-PCR and an oligonucleotide microarray method. RESULTS One FP patient had HHV-7 DNA and another had HHV-6A and -6B DNA simultaneously. In the control group, one HHV-7, one HHV-6A, and three HHV-6B DNA-positive specimens were found.
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Tikka-Kleemola P, Hämäläinen E, Tuomainen K, Suvela M, Artma A, Kahre O, Wessman M, Palotie A, Silander K. The enhancement of homogenous mass extension reaction: comparison of two enzymes. Mol Cell Probes 2007; 21:216-21. [PMID: 17331699 DOI: 10.1016/j.mcp.2006.12.003] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [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: 05/13/2006] [Revised: 12/12/2006] [Accepted: 12/21/2006] [Indexed: 10/23/2022]
Abstract
Reliable and efficient PCR and extension reactions using standardized procedures are key elements for successful single nucleotide polymorphism (SNP) genotyping projects. To improve the cost efficiency and overall performance of SNP genotyping we evaluated two commercial thermostable DNA polymerases used for the extension reaction in the homogeneous mass extension MassARRAY genotyping system. The aim was to study whether the quality, accuracy, and expenses of a new TERMIPol DNA polymerase are competitive to the commonly used ThermoSequenase DNA polymerase. We compared the enzymes by testing 96 SNPs genotyped for DNA samples of 31 unrelated individuals and one water control. The success rates, congruence between the genotypes and completeness of extension reactions support the use of TERMIPol, especially when the amplification of the higher mass allele is difficult. Further, using TERMIPol enabled successful genotyping (>93%) of several SNPs that failed (<80% success) when using ThermoSequenase.
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Affiliation(s)
- Päivi Tikka-Kleemola
- The Finnish Genome Center, P.O. Box 63, 00014 University of Helsinki, Helsinki, Finland
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Abstract
Forty-two unstable ankle joints were treated surgically by Evans' operation. The clinical postoperative results were correlated with the objective radiological stress examinations. The mean age of the patients was 29 years (15-60 years). The clinical and radiological follow-up examinations were performed 6 months after the operation. In the stress X-ray examinations a modified stress frame was used. Clinical instability was noted in four patients. In the radiological examination one patient had a pathological finding in the talar tilt test and 18 patients in the anterior drawer sign test. The radiological instability correlated poorly with the subjective end results. Six patients were estimated to have a poor result of the operation. Five of these patients had a positive anterior drawer sign in the stress X-ray examination and one had degenerative changes in the ankle. Although Evans' repair is a simple and reliable method of reconstructing ruptures of the lateral ligaments of the ankle joint, it is associated with a relatively high frequency of positive anterior subluxation on radiological stress examination. This finding can be explained by the anatomical and geometrical factors on the lateral side of the ankle joint.
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