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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] [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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Malignancy Assessment Using Gene Identification in Captured Cells Algorithm for the Prediction of Malignancy in Women With a Pelvic Mass. Obstet Gynecol 2022; 140:631-642. [PMID: 36075062 PMCID: PMC9484762 DOI: 10.1097/aog.0000000000004927] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2022] [Accepted: 06/27/2022] [Indexed: 01/05/2023]
Abstract
OBJECTIVE To evaluate the detection of malignancy in women with a pelvic mass by using multiplexed gene expression analysis of cells captured from peripheral blood. METHODS This was an IRB-approved, prospective clinical study. Eligible patients had a pelvic mass and were scheduled for surgery or biopsy. Rare cells were captured from peripheral blood obtained preoperatively by using a microfluidic cell capture device. Isolated mRNA from the captured cells was analyzed for expression of 72 different gene transcripts. Serum levels for several commonly assayed biomarkers were measured. All patients had a tissue diagnosis. Univariate and multivariate logistic regression analyses for the prediction of malignancy using gene expression and serum biomarker levels were performed, and receiver operating characteristic curves were constructed and compared. RESULTS A total of 183 evaluable patients were enrolled (average age 56 years, range 19-91 years). There were 104 benign tumors, 17 low malignant potential tumors, and 62 malignant tumors. Comparison of the area under the receiver operating characteristic curve for individual genes and various combinations of genes with or without serum biomarkers to differentiate between benign conditions (excluding low malignant potential tumors) and malignant tumors showed that a multivariate model combining the expression levels of eight genes and four serum biomarkers achieved the highest area under the curve (AUC) (95.1%, 95% CI 92.0-98.2%). The MAGIC (Malignancy Assessment using Gene Identification in Captured Cells) algorithm significantly outperformed all individual genes (AUC 50.2-65.2%; all P <.001) and a multivariate model combining 14 different genes (AUC 88.0%, 95% CI 82.9-93.0%; P =.005). Further, the MAGIC algorithm achieved an AUC of 89.5% (95% CI 81.3-97.8%) for stage I-II and 98.9% (95% CI 96.7-100%) for stage III-IV patients with epithelial ovarian cancer. CONCLUSION Multiplexed gene expression evaluation of cells captured from blood, with or without serum biomarker levels, accurately detects malignancy in women with a pelvic mass. CLINICAL TRIAL REGISTRATION ClinicalTrials.gov, NCT02781272. FUNDING SOURCE This study was funded by ANGLE Europe Limited (Surrey Research Park, Guildford, Surrey, United Kingdom).
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Relier S, Amalric A, Attina A, Koumare IB, Rigau V, Burel Vandenbos F, Fontaine D, Baroncini M, Hugnot JP, Duffau H, Bauchet L, Hirtz C, Rivals E, David A. Multivariate Analysis of RNA Chemistry Marks Uncovers Epitranscriptomics-Based Biomarker Signature for Adult Diffuse Glioma Diagnostics. Anal Chem 2022; 94:11967-11972. [PMID: 35998076 PMCID: PMC9453740 DOI: 10.1021/acs.analchem.2c01526] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
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One of the main challenges in cancer management relates
to the
discovery of reliable biomarkers, which could guide decision-making
and predict treatment outcome. In particular, the rise and democratization
of high-throughput molecular profiling technologies bolstered the
discovery of “biomarker signatures” that could maximize
the prediction performance. Such an approach was largely employed
from diverse OMICs data (i.e., genomics, transcriptomics, proteomics,
metabolomics) but not from epitranscriptomics, which encompasses more
than 100 biochemical modifications driving the post-transcriptional
fate of RNA: stability, splicing, storage, and translation. We and
others have studied chemical marks in isolation and associated them
with cancer evolution, adaptation, as well as the response to conventional
therapy. In this study, we have designed a unique pipeline combining
multiplex analysis of the epitranscriptomic landscape by high-performance
liquid chromatography coupled to tandem mass spectrometry with statistical
multivariate analysis and machine learning approaches in order to
identify biomarker signatures that could guide precision medicine
and improve disease diagnosis. We applied this approach to analyze
a cohort of adult diffuse glioma patients and demonstrate the existence
of an “epitranscriptomics-based signature” that permits
glioma grades to be discriminated and predicted with unmet accuracy.
This study demonstrates that epitranscriptomics (co)evolves along
cancer progression and opens new prospects in the field of omics molecular
profiling and personalized medicine.
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Affiliation(s)
- S Relier
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France
| | - A Amalric
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - A Attina
- IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - I B Koumare
- Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France.,Neurosurgery Department, CHU Gabriel Toure, Bamako, Mali
| | - V Rigau
- Department of Pathology and Oncobiology, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - F Burel Vandenbos
- Central Laboratory of Pathology, Univ. Côte d'Azur, CHU Nice, CNRS, INSERM, Nice, Alpes-Maritimes 06000, France
| | - D Fontaine
- Neurosurgery Department, Univ. Côte d'Azur, CHU Nice, Nice, Alpes-Maritimes 06000, France
| | - M Baroncini
- Neurosurgery Department, CHU Lille, Univ. of Lille, Lille, Nord 59037, France
| | - J P Hugnot
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France
| | - H Duffau
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - L Bauchet
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,Neurosurgery Department, Montpellier University Medical Center, Montpellier, Hérault 34295, France
| | - C Hirtz
- IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
| | - E Rivals
- LIRMM, Univ. Montpellier, CNRS, Montpellier, Hérault 34095, France
| | - A David
- IGF, Univ. Montpellier, CNRS, INSERM, Montpellier, Hérault 34094, France.,IRMB-PPC, INM, Univ Montpellier, CHU Montpellier, INSERM CNRS, Montpellier 34295, France
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Ruta graveolens L. induces death of glioblastoma cells and neural progenitors, but not of neurons, via ERK 1/2 and AKT activation. PLoS One 2015; 10:e0118864. [PMID: 25785932 PMCID: PMC4364962 DOI: 10.1371/journal.pone.0118864] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2014] [Accepted: 01/07/2015] [Indexed: 12/21/2022] Open
Abstract
Glioblastoma multiforme is a highly aggressive brain tumor whose prognosis is very poor. Due to early invasion of brain parenchyma, its complete surgical removal is nearly impossible, and even after aggressive combined treatment (association of surgery and chemo- and radio-therapy) five-year survival is only about 10%. Natural products are sources of novel compounds endowed with therapeutic properties in many human diseases, including cancer. Here, we report that the water extract of Ruta graveolens L., commonly known as rue, induces death in different glioblastoma cell lines (U87MG, C6 and U138) widely used to test novel drugs in preclinical studies. Ruta graveolens’ effect was mediated by ERK1/2 and AKT activation, and the inhibition of these pathways, via PD98058 and wortmannin, reverted its antiproliferative activity. Rue extract also affects survival of neural precursor cells (A1) obtained from embryonic mouse CNS. As in the case of glioma cells, rue stimulates the activation of ERK1/2 and AKT in A1 cells, whereas their blockade by pharmacological inhibitors prevents cell death. Interestingly, upon induction of differentiation and cell cycle exit, A1 cells become resistant to rue’s noxious effects but not to those of temozolomide and cisplatin, two alkylating agents widely used in glioblastoma therapy. Finally, rutin, a major component of the Ruta graveolens water extract, failed to cause cell death, suggesting that rutin by itself is not responsible for the observed effects. In conclusion, we report that rue extracts induce glioma cell death, discriminating between proliferating/undifferentiated and non-proliferating/differentiated neurons. Thus, it can be a promising tool to isolate novel drugs and also to discover targets for therapeutic intervention.
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