1
|
Saberi F, Youssef O, Kokkola A, Khodadoostan M, Puolakkainen P, Salehi R, Knuutila S. The frequency of NRAS mutation in stool samples of Iranian colorectal cancers compared to Finnish patients. J Res Med Sci 2024; 29:4. [PMID: 38524743 PMCID: PMC10956560 DOI: 10.4103/jrms.jrms_208_23] [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] [Subscribe] [Scholar Register] [Received: 03/30/2023] [Revised: 08/25/2023] [Accepted: 10/18/2023] [Indexed: 03/26/2024]
Abstract
Background Stools from colorectal cancer patients are noninvasive samples that could be used to compare the frequency of hotspot mutations between two different ethnic cohorts. Materials and Methods We collected stool samples from the Iranian cohort (52 patients and 49 controls) and the Finnish cohort (40 patients and 14 controls). Following stool DNA extraction, we used the AmpliSeq Colon and Lung Cancer panel to prepare DNA libraries before sequencing. Results The Iranian cohort exhibited 35 hotspot mutations in the BRAF, ERBB4, FBXW7, FGFR1, FGFR3, KRAS, MAP2K, MET, NRAS, PIK3C, SMAD4, and TP53 genes. In the Finnish cohort, 13 hotspot mutations were found in the AKT1, APC, KIT, KRAS, SMO, STK11, and TP53 genes. Mutations in NRAS and FGFR3 were observed only in the Iranian cohort, while APC mutations were exclusive for the Finnish cohort. Conclusion Genes involved in MAPK and PI3K-MAPK pathways showed a higher frequency of mutations in Iranian patients which may have therapeutic implications.
Collapse
Affiliation(s)
- Farideh Saberi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omar Youssef
- Department of Pathology, University of Helsinki, Helsinki, Finland, Europe
- Department of Clinical and Chemical Pathology, National Cancer Institute, Cairo University, Cairo, Egypt
- Research Program in Systems Oncology, Faculty of Medicine, University of Helsinki, Finland, Europe
| | - Arto Kokkola
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki, Finland, Europe
| | - Mahsa Khodadoostan
- Department of Gastroenterology and Hepatology, Alzahra Hospital, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Pauli Puolakkainen
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki, Finland, Europe
| | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
- Pediatric Inherited Diseases Research Center, Research Institute for Primordial Prevention of Noncommunicable Diseases, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sakari Knuutila
- Department of Pathology, University of Helsinki, Helsinki, Finland, Europe
| |
Collapse
|
2
|
Sammallahti H, Sarhadi VK, Kokkola A, Ghanbari R, Rezasoltani S, Asadzadeh Aghdaei H, Puolakkainen P, Knuutila S. Oncogenomic Changes in Pancreatic Cancer and Their Detection in Stool. Biomolecules 2022; 12:652. [PMID: 35625579 PMCID: PMC9171580 DOI: 10.3390/biom12050652] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2022] [Revised: 04/26/2022] [Accepted: 04/27/2022] [Indexed: 02/04/2023] Open
Abstract
Pancreatic cancer (PC) is an aggressive malignancy with a dismal prognosis. To improve patient survival, the development of screening methods for early diagnosis is pivotal. Oncogenomic alterations present in tumor tissue are a suitable target for non-invasive screening efforts, as they can be detected in tumor-derived cells, cell-free nucleic acids, and extracellular vesicles, which are present in several body fluids. Since stool is an easily accessible source, which enables convenient and cost-effective sampling, it could be utilized for the screening of these traces. Herein, we explore the various oncogenomic changes that have been detected in PC tissue, such as chromosomal aberrations, mutations in driver genes, epigenetic alterations, and differentially expressed non-coding RNA. In addition, we briefly look into the role of altered gut microbiota in PC and their possible associations with oncogenomic changes. We also review the findings of genomic alterations in stool of PC patients, and the potentials and challenges of their future use for the development of stool screening tools, including the possible combination of genomic and microbiota markers.
Collapse
Affiliation(s)
- Heidelinde Sammallahti
- Department of Pathology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Department of Surgery, Abdominal Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland; (A.K.); (P.P.)
| | - Virinder Kaur Sarhadi
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland;
| | - Arto Kokkola
- Department of Surgery, Abdominal Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland; (A.K.); (P.P.)
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran P.O. Box 1411713135, Iran;
| | - Sama Rezasoltani
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 1985717411, Iran;
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 1985717411, Iran;
| | - Pauli Puolakkainen
- Department of Surgery, Abdominal Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland; (A.K.); (P.P.)
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
| |
Collapse
|
3
|
Sammallahti H, Kokkola A, Rezasoltani S, Ghanbari R, Asadzadeh Aghdaei H, Knuutila S, Puolakkainen P, Sarhadi VK. Microbiota Alterations and Their Association with Oncogenomic Changes in Pancreatic Cancer Patients. Int J Mol Sci 2021; 22:ijms222312978. [PMID: 34884776 PMCID: PMC8658013 DOI: 10.3390/ijms222312978] [Citation(s) in RCA: 15] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/04/2021] [Revised: 11/23/2021] [Accepted: 11/25/2021] [Indexed: 02/06/2023] Open
Abstract
Pancreatic cancer (PC) is an aggressive disease with a high mortality and poor prognosis. The human microbiome is a key factor in many malignancies, having the ability to alter host metabolism and immune responses and participate in tumorigenesis. Gut microbes have an influence on physiological functions of the healthy pancreas and are themselves controlled by pancreatic secretions. An altered oral microbiota may colonize the pancreas and cause local inflammation by the action of its metabolites, which may lead to carcinogenesis. The mechanisms behind dysbiosis and PC development are not completely clear. Herein, we review the complex interactions between PC tumorigenesis and the microbiota, and especially the question, whether and how an altered microbiota induces oncogenomic changes, or vice versa, whether cancer mutations have an impact on microbiota composition. In addition, the role of the microbiota in drug efficacy in PC chemo- and immunotherapies is discussed. Possible future scenarios are the intentional manipulation of the gut microbiota in combination with therapy or the utilization of microbial profiles for the noninvasive screening and monitoring of PC.
Collapse
Affiliation(s)
- Heidelinde Sammallahti
- Department of Pathology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Department of Surgery, Abdominal Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland; (A.K.); (P.P.)
| | - Arto Kokkola
- Department of Surgery, Abdominal Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland; (A.K.); (P.P.)
| | - Sama Rezasoltani
- Foodborne and Waterborne Diseases Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 1985717411, Iran;
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Science, Tehran P.O. Box 1411713135, Iran;
| | - Hamid Asadzadeh Aghdaei
- Basic and Molecular Epidemiology of Gastrointestinal Disorders Research Center, Research Institute for Gastroenterology and Liver Diseases, Shahid Beheshti University of Medical Sciences, Tehran P.O. Box 1985717411, Iran;
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, 00014 Helsinki, Finland;
- Correspondence:
| | - Pauli Puolakkainen
- Department of Surgery, Abdominal Center, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland; (A.K.); (P.P.)
| | - Virinder Kaur Sarhadi
- Department of Oral and Maxillofacial Diseases, Helsinki University Hospital and University of Helsinki, 00290 Helsinki, Finland;
| |
Collapse
|
4
|
Sarhadi V, Mathew B, Kokkola A, Karla T, Tikkanen M, Rautelin H, Lahti L, Puolakkainen P, Knuutila S. Gut microbiota of patients with different subtypes of gastric cancer and gastrointestinal stromal tumors. Gut Pathog 2021; 13:11. [PMID: 33596997 PMCID: PMC7888145 DOI: 10.1186/s13099-021-00403-x] [Citation(s) in RCA: 18] [Impact Index Per Article: 6.0] [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] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 01/28/2021] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND Gastric adenocarcinoma is associated with H. pylori infection and inflammation that can result in the dysbiosis of gastric microbiota. The association of intestinal microbiota with gastric adenocarcinoma subtypes or with gastric gastrointestinal stromal tumors (GIST) is however not well known. Therefore, we performed 16S rRNA gene sequencing on DNA isolated from stool samples of Finnish patients and controls to study differences in microbiota among different histological subtypes of gastric adenocarcinoma, gastric GIST and healthy controls. RESULTS We found that gut microbiota alpha diversity was lowest in diffuse adenocarcinoma patients, followed by intestinal type and GIST patients, although the differences were not significant compared to controls. Beta-diversity analysis however showed significant differences in microbiota composition for all subtypes compared to controls. Significantly higher abundance of Enterobacteriaceae was observed in both adenocarcinoma subtypes, whereas lower abundance of Bifidobacteriaceae was seen only in diffuse adenocarcinoma and of Oscillibacter in intestinal adenocarcinoma. Both GIST and adenocarcinoma patients had higher abundance of Enterobacteriaceae and lower abundance of Lactobacillaceae and Oscillibacter while lower abundance of Lachnoclostridium, Bifidobacterium, Parabacteroides and Barnesiella was seen only in the adenocarcinoma patients. CONCLUSIONS Our analysis shows association of higher Enterobacteriaceae abundance with all types of gastric tumors. Therefore it could be potentially useful as a marker of gastric malignancies. Lower gut microbiota diversity might be indicative of poorly differentiated, invasive, advanced or aggressive tumors and could possibly be a prognostic marker for gastric tumors.
Collapse
Affiliation(s)
- Virinder Sarhadi
- Faculty of Medicine, Department of Pathology, University of Helsinki, 00014, Helsinki, Finland
| | - Binu Mathew
- Department of Computing, University of Turku, Turku, Finland
| | - Arto Kokkola
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki, Finland
| | | | | | - Hilpi Rautelin
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden
| | - Leo Lahti
- Department of Computing, University of Turku, Turku, Finland
| | - Pauli Puolakkainen
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki, Finland
| | - Sakari Knuutila
- Faculty of Medicine, Department of Pathology, University of Helsinki, 00014, Helsinki, Finland.
| |
Collapse
|
5
|
Sarhadi V, Lahti L, Saberi F, Youssef O, Kokkola A, Karla T, Tikkanen M, Rautelin H, Puolakkainen P, Salehi R, Knuutila S. Gut Microbiota and Host Gene Mutations in Colorectal Cancer Patients and Controls of Iranian and Finnish Origin. Anticancer Res 2020; 40:1325-1334. [PMID: 32132029 DOI: 10.21873/anticanres.14074] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [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: 01/15/2020] [Revised: 02/04/2020] [Accepted: 02/11/2020] [Indexed: 11/10/2022]
Abstract
BACKGROUND/AIM Gut microbiota plays an important role in colorectal cancer (CRC) and its composition in CRC patients can be influenced by ethnicity and tumour genomics. Herein, the aim was to study the possible associations of ethnicity and gene mutations with the gut microbiota in CRC patients. MATERIALS AND METHODS Bacterial composition in stool samples of 83 CRC patients and 60 controls from Iran and Finland was studied by 16S rRNA gene sequencing. The association of gut microbiota composition with CRC, host mutations in KRAS, NRAS and TP53, and ethnicity analysed. RESULTS Beta diversity analysis indicated significant differences between the Iranian and Finnish gut microbiota composition, in both controls and patients' groups. The Iranian controls had higher abundance of Prevotella and lower abundance of Bacteroides compared to the Finnish controls, while the Finnish patients had higher abundance of Clostridium compared to Iranian patients. Abundance of Ruminococcus was higher in patients compared to the controls. Higher abundances of Herbaspirillum, Catenibacterium and lower abundances of Barnesiella were associated with mutations in NRAS, TP53, and RAS respectively. CONCLUSION A possible link of host gene mutations with gut bacterial composition is suggested.
Collapse
Affiliation(s)
- Virinder Sarhadi
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Leo Lahti
- Department of Future Technologies, University of Turku, Turku, Finland
| | - Farideh Saberi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Omar Youssef
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Arto Kokkola
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki, Finland
| | | | | | - Hilpi Rautelin
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, Uppsala, Sweden
| | | | - Rasoul Salehi
- Department of Genetics and Molecular Biology, School of Medicine, Isfahan University of Medical Sciences, Isfahan, Iran.,Pediatric Inherited Diseases Research Center, Isfahan University of Medical Sciences, Isfahan, Iran
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| |
Collapse
|
6
|
Bao J, Walliander M, Kovács F, Nagaraj AS, Hemmes A, Sarhadi VK, Knuutila S, Lundin J, Horvath P, Verschuren EW. Spa-RQ: an Image Analysis Tool to Visualise and Quantify Spatial Phenotypes Applied to Non-Small Cell Lung Cancer. Sci Rep 2019; 9:17613. [PMID: 31772293 PMCID: PMC6879493 DOI: 10.1038/s41598-019-54038-9] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [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: 02/20/2019] [Accepted: 11/06/2019] [Indexed: 12/14/2022] Open
Abstract
To facilitate analysis of spatial tissue phenotypes, we created an open-source tool package named ‘Spa-RQ’ for ‘Spatial tissue analysis: image Registration & Quantification’. Spa-RQ contains software for image registration (Spa-R) and quantitative analysis of DAB staining overlap (Spa-Q). It provides an easy-to-implement workflow for serial sectioning and staining as an alternative to multiplexed techniques. To demonstrate Spa-RQ’s applicability, we analysed the spatial aspects of oncogenic KRAS-related signalling activities in non-small cell lung cancer (NSCLC). Using Spa-R in conjunction with ImageJ/Fiji, we first performed annotation-guided tumour-by-tumour phenotyping using multiple signalling markers. This analysis showed histopathology-selective activation of PI3K/AKT and MAPK signalling in Kras mutant murine tumours, as well as high p38MAPK stress signalling in p53 null murine NSCLC. Subsequently, Spa-RQ was applied to measure the co-activation of MAPK, AKT, and their mutual effector mTOR pathway in individual tumours. Both murine and clinical NSCLC samples could be stratified into ‘MAPK/mTOR’, ‘AKT/mTOR’, and ‘Null’ signature subclasses, suggesting mutually exclusive MAPK and AKT signalling activities. Spa-RQ thus provides a robust and easy to use tool that can be employed to identify spatially-distributed tissue phenotypes.
Collapse
Affiliation(s)
- Jie Bao
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Margarita Walliander
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | | | - Ashwini S Nagaraj
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Annabrita Hemmes
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland
| | - Virinder Kaur Sarhadi
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Johan Lundin
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland.,Department of Public Health Sciences, Karolinska Institutet, Stockholm, Sweden
| | - Peter Horvath
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland.,Synthetic and Systems Biology Unit, Hungarian Academy of Sciences, Biological Research Center, Temesvári körút 62, 6726, Szeged, Hungary
| | - Emmy W Verschuren
- Institute for Molecular Medicine Finland (FIMM), HiLIFE, University of Helsinki, Helsinki, 00014, Finland.
| |
Collapse
|
7
|
Narvi E, Vaparanta K, Karrila A, Chakroborty D, Knuutila S, Pulliainen A, Sundvall M, Elenius K. Different responses of colorectal cancer cells to alternative sequences of cetuximab and oxaliplatin. Sci Rep 2018; 8:16579. [PMID: 30410004 PMCID: PMC6224565 DOI: 10.1038/s41598-018-34938-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [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: 05/10/2018] [Accepted: 10/29/2018] [Indexed: 11/14/2022] Open
Abstract
Therapeutic protocols including EGFR antibodies in the context of oxaliplatin-based regimens have variable clinical effect in colorectal cancer. Here, we tested the effect of the EGFR antibody cetuximab in different sequential combinations with oxaliplatin on the growth of colorectal cancer cells in vitro and in vivo. Cetuximab reduced the efficacy of oxaliplatin when administered before oxaliplatin but provided additive effect when administered after oxaliplatin regardless of the KRAS or BRAF mutation status of the cells. Systemic gene expression and protein phosphorylation screens revealed alternatively activated pathways regulating apoptosis, cell cycle and DNA damage response. Functional assays indicated that cetuximab-induced arrest of the cells into the G1 phase of the cell cycle was associated with reduced responsiveness of the cells to subsequent treatment with oxaliplatin. In contrast, oxaliplatin-enhanced responsiveness to subsequent treatment with cetuximab was associated with increased apoptosis, inhibition of STAT3 activity and increased EGFR down-regulation. This preclinical study indicates that optimizing the sequence of administration may enhance the antitumor effect of combination therapy with EGFR antibodies and oxaliplatin.
Collapse
Affiliation(s)
- Elli Narvi
- Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Turku, Finland
| | - Katri Vaparanta
- Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, Turku, Finland
| | - Anna Karrila
- Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, Turku, Finland
| | - Deepankar Chakroborty
- Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Turku, Finland.,Turku Doctoral Programme of Molecular Medicine, Turku, Finland
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | - Arto Pulliainen
- Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Turku, Finland
| | - Maria Sundvall
- Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Turku, Finland.,Department of Oncology, Turku University Hospital, Turku, Finland
| | - Klaus Elenius
- Institute of Biomedicine and Medicity Research Laboratories, University of Turku, Turku, Finland. .,Department of Oncology, Turku University Hospital, Turku, Finland.
| |
Collapse
|
8
|
Youssef O, Lahti L, Kokkola A, Karla T, Tikkanen M, Ehsan H, Carpelan-Holmström M, Koskensalo S, Böhling T, Rautelin H, Puolakkainen P, Knuutila S, Sarhadi V. Stool Microbiota Composition Differs in Patients with Stomach, Colon, and Rectal Neoplasms. Dig Dis Sci 2018; 63:2950-2958. [PMID: 29995183 PMCID: PMC6182444 DOI: 10.1007/s10620-018-5190-5] [Citation(s) in RCA: 57] [Impact Index Per Article: 9.5] [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: 11/27/2017] [Accepted: 06/28/2018] [Indexed: 12/12/2022]
Abstract
BACKGROUND Microbial ecosystems that inhabit the human gut form central component of our physiology and metabolism, regulating and modulating both health and disease. Changes or disturbances in the composition and activity of this gut microbiota can result in altered immunity, inflammation, and even cancer. AIM To compare the composition and diversity of gut microbiota in stool samples from patient groups based on the site of neoplasm in the gastrointestinal tract (GIT) and to assess the possible contribution of the bacterial composition to tumorigenesis. METHODS We studied gut microbiota by16S RNA gene sequencing from stool DNA of 83 patients, who were diagnosed with different GIT neoplasms, and 13 healthy individuals. RESULTS As compared to healthy individuals, stools of patients with stomach neoplasms had elevated levels of Enterobacteriaceae, and those with rectal neoplasms had lower levels of Bifidobacteriaceae. Lower abundance of Lactobacillaceae was seen in patients with colon neoplasms. Abundance of Lactobacillaceae was higher in stools of GIT patients sampled after cancer treatment compared to samples collected before start of any treatment. In addition to site-specific differences, higher abundances of Ruminococcus, Subdoligranulum and lower abundances of Lachnoclostridium and Oscillibacter were observed in overall GIT neoplasms as compared to healthy controls CONCLUSION: Our study demonstrates that the alterations in gut microbiota vary according to the site of GIT neoplasm. The observed lower abundance of two common families, Lactobacillaceae and Bifidobacteriaceae, and the increased abundance of Enterobacteriaceae could provide indicators of compromised gut health and potentially facilitate GIT disease monitoring.
Collapse
Affiliation(s)
- Omar Youssef
- Department of Pathology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014 Helsinki, Finland
| | - Leo Lahti
- Department of Mathematics and Statistics, University of Turku, 20014 Turku, Finland
| | - Arto Kokkola
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, 00290 Helsinki, Finland
| | - Tiina Karla
- Thermo Fisher Scientific Company, 01620 Vantaa, Finland
| | | | - Homa Ehsan
- Department of Pathology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014 Helsinki, Finland
| | | | - Selja Koskensalo
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, 00290 Helsinki, Finland
| | - Tom Böhling
- Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, 00014 Helsinki, Finland
| | - Hilpi Rautelin
- Department of Medical Sciences, Clinical Microbiology, Uppsala University, 751 85 Uppsala, Sweden
| | - Pauli Puolakkainen
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, 00290 Helsinki, Finland
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014 Helsinki, Finland
| | - Virinder Sarhadi
- Department of Pathology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, 00014 Helsinki, Finland
| |
Collapse
|
9
|
Youssef O, Sarhadi V, Ehsan H, Böhling T, Carpelan-Holmström M, Koskensalo S, Puolakkainen P, Kokkola A, Knuutila S. Gene mutations in stool from gastric and colorectal neoplasia patients by next-generation sequencing. World J Gastroenterol 2017; 23:8291-8299. [PMID: 29307989 PMCID: PMC5743500 DOI: 10.3748/wjg.v23.i47.8291] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 10/03/2017] [Revised: 11/01/2017] [Accepted: 11/14/2017] [Indexed: 02/06/2023] Open
Abstract
AIM To study cancer hotspot mutations by next-generation sequencing (NGS) in stool DNA from patients with different gastrointestinal tract (GIT) neoplasms.
METHODS Stool samples were collected from 87 Finnish patients diagnosed with various gastric and colorectal neoplasms, including benign tumors, and from 14 healthy controls. DNA was isolated from stools by using the PSP® Spin Stool DNA Plus Kit. For each sample, 20 ng of DNA was used to construct sequencing libraries using the Ion AmpliSeq Cancer Hotspot Panel v2 or Ion AmpliSeq Colon and Lung Cancer panel v2. Sequencing was performed on Ion PGM. Torrent Suite Software v.5.2.2 was used for variant calling and data analysis.
RESULTS NGS was successful in assaying 72 GIT samples and 13 healthy controls, with success rates of the assay being 78% for stomach neoplasia and 87% for colorectal tumors. In stool specimens from patients with gastric neoplasia, five hotspot mutations were found in APC, CDKN2A and EGFR genes, in addition to seven novel mutations. From colorectal patients, 20 mutations were detected in AKT1, APC, ERBB2, FBXW7, KIT, KRAS, NRAS, SMARCB1, SMO, STK11 and TP53. Healthy controls did not exhibit any hotspot mutations, except for two novel ones. APC and TP53 were the most frequently mutated genes in colorectal neoplasms, with five mutations, followed by KRAS with two mutations. APC was the most commonly mutated gene in stools of patients with premalignant/benign GIT lesions.
CONCLUSION Our results show that in addition to colorectal neoplasms, mutations can also be assayed from stool specimens of patients with gastric neoplasms.
Collapse
Affiliation(s)
- Omar Youssef
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Virinder Sarhadi
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Homa Ehsan
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| | - Tom Böhling
- Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki 00014, Finland
| | | | - Selja Koskensalo
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki 00290, Finland
| | - Pauli Puolakkainen
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki 00290, Finland
| | - Arto Kokkola
- The HUCH Gastrointestinal Clinic, University Central Hospital of Helsinki, Helsinki 00290, Finland
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki 00014, Finland
| |
Collapse
|
10
|
Mosakhani N, Sarhadi V, Panula P, Partinen M, Knuutila S. Narcolepsy patients' blood-based miRNA expression profiling: miRNA expression differences with Pandemrix vaccination. Acta Neurol Scand 2017; 136:462-469. [PMID: 28251619 DOI: 10.1111/ane.12749] [Citation(s) in RCA: 5] [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] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 12/16/2016] [Indexed: 12/17/2022]
Abstract
OBJECTIVES Narcolepsy is a neurological sleep disorder characterized by excessive daytime sleepiness and nighttime sleep disturbance. Among children and adolescents vaccinated with Pandemrix vaccine in Finland and Sweden, the number of narcolepsy cases increased. Our aim was to identify miRNAs involved in narcolepsy and their association with Pandemrix vaccination. MATERIALS AND METHODS We performed global miRNA proofing by miRNA microarrays followed by RT-PCR verification on 20 narcolepsy patients (Pandemrix-associated and Pandemrix-non-associated) and 17 controls (vaccinated and non-vaccinated). RESULTS Between all narcolepsy patients and controls, 11 miRNAs were differentially expressed; 17 miRNAs showed significantly differential expression between Pandemrix-non-associated narcolepsy patients and non-vaccinated healthy controls. MiR-188-5p and miR-4499 were over-expressed in narcolepsy patients vs healthy controls. Two miRNAs, miR-1470 and miR-4455, were under-expressed in Pandemrix-associated narcolepsy patients vs Pandemrix-non-associated narcolepsy patients. CONCLUSIONS We identified miRNA expression patterns in narcolepsy patients that linked them to mRNA targets known to be involved in brain-related pathways or brain disorders.
Collapse
Affiliation(s)
- N. Mosakhani
- Department of Pathology; University of Helsinki; Helsinki Finland
| | - V. Sarhadi
- Department of Pathology; University of Helsinki; Helsinki Finland
| | - P. Panula
- Neuroscience Center; Biomedicum; University of Helsinki; Helsinki Finland
| | - M. Partinen
- Department of Clinical Neurosciences; University of Helsinki; Helsinki Finland
- Helsinki Sleep Clinic; Vitalmed Research Center; Helsinki Finland
| | - S. Knuutila
- Department of Pathology; University of Helsinki; Helsinki Finland
| |
Collapse
|
11
|
Youssef O, Knuuttila A, Piirilä P, Böhling T, Sarhadi V, Knuutila S. Detection of cancer associated mutations in exhaled breath condensates of healthy subjects by next generation sequencing. Ann Oncol 2017. [DOI: 10.1093/annonc/mdx508.025] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/12/2022] Open
|
12
|
Youssef O, Knuuttila A, Piirilä P, Böhling T, Sarhadi V, Knuutila S. Presence of cancer-associated mutations in exhaled breath condensates of healthy individuals by next generation sequencing. Oncotarget 2017; 8:18166-18176. [PMID: 28199989 PMCID: PMC5392316 DOI: 10.18632/oncotarget.15233] [Citation(s) in RCA: 16] [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] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2016] [Accepted: 01/16/2017] [Indexed: 01/29/2023] Open
Abstract
Exhaled breath condensate (EBC) is a non-invasive source that can be used for studying different genetic alterations occurring in lung tissue. However, the low yield of DNA available from EBC has hampered the more detailed mutation analysis by conventional methods. We applied the more sensitive amplicon-based next generation sequencing (NGS) to identify cancer related mutations in DNA isolated from EBC. In order to apply any method for the purpose of mutation screening in cancer patients, it is important to clarify the incidence of these mutations in healthy individuals. Therefore, we studied mutations in hotspot regions of 22 cancer genes of 20 healthy, mainly non-smoker individuals, using AmpliSeq colon and lung cancer panel and sequenced on Ion PGM. In 15 individuals, we detected 35 missense mutations in TP53, KRAS, NRAS, SMAD4, MET, CTNNB1, PTEN, BRAF, DDR2, EGFR, PIK3CA, NOTCH1, FBXW7, FGFR3, and ERBB2: these have been earlier reported in different tumor tissues. Additionally, 106 novel mutations not reported previously were also detected. One healthy non-smoker subject had a KRAS G12D mutation in EBC DNA. Our results demonstrate that DNA from EBC of healthy subjects can reveal mutations that could represent very early neoplastic changes or alternatively a normal process of apoptosis eliminating damaged cells with mutations or altered genetic material. Further assessment is needed to determine if NGS analysis of EBC could be a screening method for high risk individuals such as smokers, where it could be applied in the early diagnosis of lung cancer and monitoring treatment efficacy.
Collapse
Affiliation(s)
- Omar Youssef
- Faculty of Medicine, Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Aija Knuuttila
- Department of Pulmonary Medicine, University of Helsinki and Helsinki University Hospital, Heart and Lung Center, Helsinki, Finland
| | - Päivi Piirilä
- Unit of Clinical Physiology, HUS-Medical Imaging Center, Helsinki University Hospital and Helsinki University, Helsinki, Finland
| | - Tom Böhling
- Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, Helsinki, Finland
| | - Virinder Sarhadi
- Faculty of Medicine, Department of Pathology, University of Helsinki, Helsinki, Finland
| | - Sakari Knuutila
- Faculty of Medicine, Department of Pathology, University of Helsinki, Helsinki, Finland
| |
Collapse
|
13
|
Veija T, Koljonen V, Bohling T, Kero M, Knuutila S, Sarhadi VK. Aberrant expression of ALK and EZH2 in Merkel cell carcinoma. BMC Cancer 2017; 17:236. [PMID: 28359267 PMCID: PMC5374569 DOI: 10.1186/s12885-017-3233-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2016] [Accepted: 03/24/2017] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Distinct characteristic features categorize Merkel cell carcinoma (MCC) into two subgroups according to the Merkel cell polyomavirus infection. Many mutational studies on MCC have been carried out in recent years without identifying a prominent driver mutation. However, there is paucity reporting the expression of cancer genes at the RNA level in MCC tumors. In this study, we studied the RNA expression profiles of 26 MCC tumors, with a goal to identify prospective molecular targets that could improve the treatment strategies of MCC. METHODS RNA expression of 50 cancer-related genes in 26 MCC tumors was analyzed by targeted amplicon based next-generation sequencing using the Ion Torrent technology and the expression compared with that of normal, non-cancerous skin samples. Sequencing data were processed using Torrent Suite™ Software. Expression profiles of MCV-negative and MCV-positive tumors were compared. Fluorescence in situ hybridization was performed to study ALK rearrangements and immunohistochemistry to study ALK expression in tumor tissue. RESULTS ALK, CDKN2A, EZH2 and ERBB4 were overexpressed, and EGFR, ERBB2, PDGFRA and FGFR1 were underexpressed in MCC tumors compared to normal skin. In the MCV-negative tumors, MET, NOTCH1, FGFR3, and SMO were overexpressed and JAK3 and NPM1 were under-expressed compared to the MCV-positive tumors. CONCLUSIONS High expression of ALK, CDKN2A and EZH2 was recorded in MCC tumors. No ALK fusion was seen by FISH analysis. Overexpression of EZH2 suggests its potential as a drug target in MCC.
Collapse
Affiliation(s)
- Tuukka Veija
- Department of Pathology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland.
| | - Virve Koljonen
- Department of Plastic Surgery, University of Helsinki and Helsinki University Hospital, Topeliuksenkatu 5, P.O. Box 266, FI-00029, Helsinki, Finland
| | - Tom Bohling
- Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland
| | - Mia Kero
- Department of Pathology, University of Helsinki and HUSLAB, Helsinki University Hospital, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland
| | - Virinder Kaur Sarhadi
- Department of Pathology, Faculty of Medicine, University of Helsinki, Haartmaninkatu 3, P.O. Box 21, FI-00014, Helsinki, Finland
| |
Collapse
|
14
|
Caliò A, Bria E, Pilotto S, Gilioli E, Nottegar A, Eccher A, Cima L, Santo A, Pedron S, Turri G, Knuutila S, Chilosi M, Vanzo F, Bogina G, Terzi A, Tortora G, Scarpa A, Loda M, Martignoni G, Brunelli M. ALK gene copy number in lung cancer: Unspecific polyploidy versus specific amplification visible as double minutes. Cancer Biomark 2017; 18:215-220. [PMID: 28009326 DOI: 10.3233/cbm-161680] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Abstract
BACKGROUND Gains of a gene due to DNA polyploidy versus amplification of the specific locus are distinct molecular alterations in tumors. OBJECTIVE We quantified copy number gains of ALK gene due to unspecific polyploidy versus amplifications of the specific locus in a series of non-small cell lung cancers. METHODS The locus specific ALK copy (LSI) number status was evaluated in 205 cases by FISH. Ratio LSI ALK copy number corrected for control probes CEP2, CEP3 and CEP17 (CEPs) was scored. Amplification of the specific ALK locus was defined when ratio set to ≥ 2 while polyploidy was interpreted when the increase in gene copy resulted < 2 in ratio (LSI/control CEPs). RESULTS Twenty one cases (10.2%) showed ≥ 8 ALK signals, 68 cases (33.2%) 3-7 signals and 116 cases (56.6%) a mean of 2 signals. Only 2/21 cases of the cohort harboring ≥ 8 signals showed a ratio ≥ 2 after CEPs correction interpretable as amplified, showing numerous doubled fluorescent spots. All the remaining cases showed a mirrored number of fluorescent spots per each CEPs, interpretable as polyploidy. CONCLUSION We detected a high prevalence of ALK gene copy number usually due to polyploidy rather than ALK locus amplification, the latter visible prevalently as double minutes.
Collapse
Affiliation(s)
- Anna Caliò
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Emilio Bria
- Medical Oncology, University and Hospital Trust, Verona, Italy
| | - Sara Pilotto
- Medical Oncology, University and Hospital Trust, Verona, Italy
| | - Eliana Gilioli
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Alessia Nottegar
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Albino Eccher
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Luca Cima
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Antonio Santo
- Medical Oncology, University and Hospital Trust, Verona, Italy
| | - Serena Pedron
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Giona Turri
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Sakari Knuutila
- Department of Pathology, Laboratory of Molecular Cytogenetic, University of Helsinki, Helsinki, Finland
| | - Marco Chilosi
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Francesca Vanzo
- Arsenàl, Veneto's Research Center for eHealth Innovation, Veneto, Italy
| | | | - Alberto Terzi
- Thoracic Surgery, SacroCuore Hospital, Negrar, Italy
| | | | - Aldo Scarpa
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| | - Massimo Loda
- Dana-Farber Cancer Institute, Harvard Medical School, Brigham And Women's Hospital, Boston, MA, USA
| | - Guido Martignoni
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy.,Anatomic Pathology, Pederzoli Hospital, Peschiera Del Garda, Verona, Italy
| | - Matteo Brunelli
- Department of Diagnostics and Public Health, Anatomic Pathology, University and Hospital Trust, Verona, Italy
| |
Collapse
|
15
|
Ghanbari R, Rezasoltani S, Hashemi J, Mohamadkhani A, Tahmasebifar A, Arefian E, Mobarra N, Asadi J, Nazemalhosseini Mojarad E, Yazdani Y, Knuutila S, Malekzadeh R. Expression Analysis of Previously Verified Fecal and Plasma Dow-regulated MicroRNAs (miR-4478, 1295-3p, 142-3p and 26a-5p), in FFPE Tissue Samples of CRC Patients. Arch Iran Med 2017; 20:92-95. [PMID: 28193082 DOI: 0172002/aim.006] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
BACKGROUND Colorectal cancer (CRC) is one of the most common causes of cancer-related mortality worldwide. Early diagnosis of this neoplasm is critical and may reduce patients' mortality. MicroRNAs are small non-coding RNA molecules whose expression pattern can be altered in various diseases such as CRC. METHODS In this study, we evaluated the expression levels of miR-142-3p, miR-26a-5p (their reduced expression in plasma samples of CRC patients was previously confirmed), miR-4478 and miR-1295-3p (their reduced expression in stool samples of CRC patients was previously confirmed) in tissue samples of CRC patients in comparison to healthy subjects. To achieve this purpose, total RNA including small RNA was extracted from 53 CRC and 35 normal subjects' Formalin-fixed, Paraffin-embedded (FFPE) tissue samples using the miRNeasy FFPE Mini Kit. The expression levels of these four selected miRNAs were measured using quantitative Reverse Transcriptase Polymerase Chain Reaction (qRT-PCR). RESULTS We found that the expression levels of miR-4478 and miR-1295b-3p (two previously down-regulated fecal miRNAs) were significantly decreased in FFPE samples of CRC patients compared to healthy controls. On the other hand, no significant differences were seen in expression levels of miR-142-3p and miR-26a-5p (two previously down-regulated circulating miRNAs) in FFPE samples between these two groups. CONCLUSION Regarding current findings, it may be concluded that to diagnose CRC patients based on the miRNAs approach, stool samples are more likely preferable to plasma samples; nevertheless, additional studies with more samples are needed to confirm the results.
Collapse
Affiliation(s)
- Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sama Rezasoltani
- Department of Biology, Science and Research Branch, Islamic Azad University, Tehran, Iran
| | - Javad Hashemi
- Department of Clinical Biochemistry, Tehran University of Medical Sciences, Tehran, Iran
| | - Ashraf Mohamadkhani
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Arash Tahmasebifar
- Department of Molecular Medicine and Nanomedicine, Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences (GOUMS), Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, 14155-6455, Tehran, Iran
| | - Naser Mobarra
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Jahanbakhsh Asadi
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Ehsan Nazemalhosseini Mojarad
- Gastroenterology and Liver Disease Research Center, Research Institute for Gastroenterology and Liver Dseases, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Yaghoub Yazdani
- Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute, Helsinki University, Helsinki, Finland
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| |
Collapse
|
16
|
Mäki-Nevala S, Sarhadi VK, Knuuttila A, Scheinin I, Ellonen P, Lagström S, Rönty M, Kettunen E, Husgafvel-Pursiainen K, Wolff H, Knuutila S. Driver Gene and Novel Mutations in Asbestos-Exposed Lung Adenocarcinoma and Malignant Mesothelioma Detected by Exome Sequencing. Lung 2016; 194:125-35. [PMID: 26463840 DOI: 10.1007/s00408-015-9814-7] [Citation(s) in RCA: 32] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2015] [Accepted: 09/27/2015] [Indexed: 12/30/2022]
Abstract
BACKGROUND Asbestos is a carcinogen linked to malignant mesothelioma (MM) and lung cancer. Some gene aberrations related to asbestos exposure are recognized, but many associated mutations remain obscure. We performed exome sequencing to determine the association of previously known mutations (driver gene mutations) with asbestos and to identify novel mutations related to asbestos exposure in lung adenocarcinoma (LAC) and MM. METHODS Exome sequencing was performed on DNA from 47 tumor tissues of MM (21) and LAC (26) patients, 27 of whom had been asbestos-exposed (18 MM, 9 LAC). In addition, 9 normal lung/blood samples of LAC were sequenced. Novel mutations identified from exome data were validated by amplicon-based deep sequencing. Driver gene mutations in BRAF, EGFR, ERBB2, HRAS, KRAS, MET, NRAS, PIK3CA, STK11, and ephrin receptor genes (EPHA1-8, 10 and EPHB1-4, 6) were studied for both LAC and MM, and in BAP1, CUL1, CDKN2A, and NF2 for MM. RESULTS In asbestos-exposed MM patients, previously non-described NF2 frameshift mutation (one) and BAP1 mutations (four) were detected. Exome data mining revealed some genes potentially associated with asbestos exposure, such as MRPL1 and SDK1. BAP1 and COPG1 mutations were seen exclusively in MM. Pathogenic KRAS mutations were common in LAC patients (42 %), both in non-exposed (n = 5) and exposed patients (n = 6). Pathogenic BRAF mutations were found in two LACs. CONCLUSION BAP1 mutations occurred in asbestos-exposed MM. MRPL1, SDK1, SEMA5B, and INPP4A could possibly serve as candidate genes for alterations associated with asbestos exposure. KRAS mutations in LAC were not associated with asbestos exposure.
Collapse
|
17
|
Martignoni G, Brunelli M, Segala D, Munari E, Gobbo S, Cima L, Borze I, Wirtanen T, Sarhadi VK, Atanesyan L, Savola S, Barzon L, Masi G, Fassan M, Eble JN, Bohling T, Cheng L, Delahunt B, Knuutila S. Validation of 34betaE12 immunoexpression in clear cell papillary renal cell carcinoma as a sensitive biomarker. Pathology 2016; 49:10-18. [PMID: 27923499 DOI: 10.1016/j.pathol.2016.05.014] [Citation(s) in RCA: 14] [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: 04/27/2016] [Accepted: 05/22/2016] [Indexed: 02/07/2023]
Abstract
Clear cell papillary renal cell carcinoma (CCPRCC) is a recently recognised neoplasm with a broad spectrum of morphological characteristics, thus representing a challenging differential diagnosis, especially with the low malignant potential multicystic renal cell neoplasms and clear cell renal cell carcinoma. We selected 14 cases of CCPRCC with a wide spectrum of morphological features diagnosed on morphology and CK7 immunoreactivity and analysed them using a panel of immunohistochemical markers, focusing on 34βE12 and related CKs 1,5,10 and 14 and several molecular analyses such as fluorescence in situ hybridisation (FISH), array comparative genomic hybridisation (aCGH), VHL methylation, VHL and TCEB1 sequencing and multiplex ligation-dependent probe amplification (MLPA). Twelve of 13 (92%) CCPRCC tumours were positive for 34βE12. One tumour without 3p alteration by FISH revealed VHL mutation and 3p deletion at aCGH; thus, it was re-classified as clear cell RCC. We concluded that: (1) immunohistochemical expression of CK7 is necessary for diagnostic purposes, but may not be sufficient to identify CCPRCC, while 34βE12, in part due to the presence of CK14 antigen expression, can be extremely useful for the recognition of this tumour; and (2) further molecular analysis of chromosome 3p should be considered to support of CCPRCC diagnosis, when FISH analysis does not evidence the common loss of chromosome 3p.
Collapse
Affiliation(s)
- Guido Martignoni
- Department of Pathology and Diagnostics, Anatomic Pathology, University and Hospital Trust of Verona, Verona, Italy; Pederzoli Hospital, Anatomic Pathology, Peschiera del Garda, Verona, Italy.
| | - Matteo Brunelli
- Department of Pathology and Diagnostics, Anatomic Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Diego Segala
- Pederzoli Hospital, Anatomic Pathology, Peschiera del Garda, Verona, Italy
| | - Enrico Munari
- Department of Pathology and Diagnostics, Anatomic Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Stefano Gobbo
- Pederzoli Hospital, Anatomic Pathology, Peschiera del Garda, Verona, Italy
| | - Luca Cima
- Department of Pathology and Diagnostics, Anatomic Pathology, University and Hospital Trust of Verona, Verona, Italy
| | - Ioana Borze
- Hartmann Institute and HUSLab, University of Helsinki, Department of Pathology, Helsinki, Finland
| | - Tina Wirtanen
- Hartmann Institute and HUSLab, University of Helsinki, Department of Pathology, Helsinki, Finland
| | - Virinder Kaur Sarhadi
- Hartmann Institute and HUSLab, University of Helsinki, Department of Pathology, Helsinki, Finland
| | | | | | - Luisa Barzon
- Histology, Microbiology and Medical Biotechnologies, University of Padua, Padua, Italy
| | - Giulia Masi
- Histology, Microbiology and Medical Biotechnologies, University of Padua, Padua, Italy
| | - Matteo Fassan
- Department of Pathology, Anatomic Pathology, University of Padua, Padua, Italy
| | - John N Eble
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Tom Bohling
- Hartmann Institute and HUSLab, University of Helsinki, Department of Pathology, Helsinki, Finland
| | - Liang Cheng
- Department of Pathology and Laboratory Medicine, Indiana University School of Medicine, Indianapolis, Indiana, United States
| | - Brett Delahunt
- Wellington School of Medicine and Health Sciences, Department of Pathology and Molecular Medicine, University of Otago, Wellington, New Zealand
| | - Sakari Knuutila
- Hartmann Institute and HUSLab, University of Helsinki, Department of Pathology, Helsinki, Finland
| |
Collapse
|
18
|
Heikinheimo K, Jee KJ, Morgan PR, Nagy B, Knuutila S, Leivo I. Genetic Changes in Sporadic Keratocystic Odontogenic Tumors (Odontogenic Keratocysts). J Dent Res 2016; 86:544-9. [PMID: 17525355 DOI: 10.1177/154405910708600611] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
Abstract
Little is known about the genetic background of keratocystic odontogenic tumors (KCOT, odontogenic keratocysts). Our aim was to characterize genomic aberrations in sporadic KCOT using cDNA-expression arrays and array-comparative genomic hybridization. For cDNA-expression arrays, 10 KCOT specimens and 20 fetal tooth germs were studied. Quantitative real-time reverse-transcription/polymerase chain-reaction and immunohistochemical studies were also undertaken. Several genes were over-expressed in 12q13, including cytokeratin 6B ( KRT6B) (≈ 10-fold), epidermal growth factor receptor ERBB3 (~ 4.7-fold), and glioma-associated oncogene homologue 1 ( GLI1) (~ 5- to 12-fold). One amplicon (~ 0.7 Mega base pairs [Mbp]), covering several genes involved in the regulation of cell growth, was found in 12q13.2. Deletions were found in 3q13.1, 5p14.3, and 7q31.3, including the cell-adhesion-related gene cadherin 18 ( CDH18) and leukocyte cell adhesion molecule ( ALCAM, MEMD). Over-expressed and amplified genes in 12q13, also reported in several other tumors and cell lines, may contribute to the persistent growth characteristics of KCOT.
Collapse
Affiliation(s)
- K Heikinheimo
- Department of Oral and Maxillofacial Surgery, Institute of Dentistry, University of Turku, Lemminkäisenkatu 2, FIN-20520 Turku, Finland.
| | | | | | | | | | | |
Collapse
|
19
|
Mäki-Nevala S, Sarhadi VK, Rönty M, Kettunen E, Husgafvel-Pursiainen K, Wolff H, Knuuttila A, Knuutila S. Hot spot mutations in Finnish non-small cell lung cancers. Lung Cancer 2016; 99:102-10. [DOI: 10.1016/j.lungcan.2016.06.024] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2016] [Revised: 06/07/2016] [Accepted: 06/27/2016] [Indexed: 12/22/2022]
|
20
|
Youssef O, Sarhadi VK, Armengol G, Piirilä P, Knuuttila A, Knuutila S. Exhaled breath condensate as a source of biomarkers for lung carcinomas. A focus on genetic and epigenetic markers-A mini-review. Genes Chromosomes Cancer 2016; 55:905-914. [DOI: 10.1002/gcc.22399] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/18/2016] [Revised: 07/26/2016] [Accepted: 07/27/2016] [Indexed: 12/12/2022] Open
Affiliation(s)
- Omar Youssef
- Faculty of Medicine; Department of Pathology, University of Helsinki; Helsinki Finland
| | - Virinder Kaur Sarhadi
- Faculty of Medicine; Department of Pathology, University of Helsinki; Helsinki Finland
| | - Gemma Armengol
- Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Universitat Autònoma De Barcelona; Barcelona Catalonia Spain
| | - Päivi Piirilä
- Unit of Clinical Physiology, HUS-Medical Imaging Center, Helsinki University Hospital and Helsinki University; Helsinki Finland
| | - Aija Knuuttila
- Department of Pulmonary Medicine; University of Helsinki and Helsinki University Hospital, Heart and Lung Center; Helsinki Finland
| | - Sakari Knuutila
- Faculty of Medicine; Department of Pathology, University of Helsinki; Helsinki Finland
| |
Collapse
|
21
|
Kaartokallio T, Lokki AI, Peterson H, Kivinen K, Hiltunen L, Salmela E, Lappalainen T, Maanselkä P, Heino S, Knuutila S, Sayed A, Poston L, Brennecke SP, Johnson MP, Morgan L, Moses EK, Kere J, Laivuori H. Preeclampsia does not share common risk alleles in 9p21 with coronary artery disease and type 2 diabetes. Ann Med 2016; 48:330-6. [PMID: 27111527 DOI: 10.1080/07853890.2016.1174877] [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] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Indexed: 01/08/2023] Open
Abstract
INTRODUCTION Preeclampsia is a common and partially genetic pregnancy complication characterized by hypertension and proteinuria. Association with cardiovascular disease and type 2 diabetes has been reported in 9p21 by several genome-wide association studies. It has been hypothesized that cardiometabolic diseases may share common etiology with preeclampsia. MATERIALS AND METHODS We tested association with the 9p21 region to preeclampsia in the Finnish population by genotyping 23 tagging single nucleotide polymorphisms (SNPs) in 15 extended preeclampsia families and in a nationwide cohort consisting of 281 cases and 349 matched controls. Replication was conducted in additional datasets. RESULTS Four SNPs (rs7044859, rs496892, rs564398 and rs7865618) showed nominal association (p ≤ 0.024 uncorrected) with preeclampsia in the case-control cohort. To increase power, we genotyped two SNPs in additional 388 cases and 341 controls from the Finnish Genetics of Preeclampsia Consortium (FINNPEC) cohort. Partial replication was also attempted in a UK cohort (237 cases and 199 controls) and in 74 preeclamptic families from Australia/New Zealand. We were unable to replicate the initial association in the extended Finnish dataset or in the two international cohorts. CONCLUSIONS Our study did not find evidence for the involvement of the 9p21 region in the risk of preeclampsia. Key Message Chromosome 9p21 is not associated with preeclampsia.
Collapse
Affiliation(s)
- Tea Kaartokallio
- a Medical and Clinical Genetics , University of Helsinki and Helsinki University Hospital , Helsinki , Finland
| | - A Inkeri Lokki
- a Medical and Clinical Genetics , University of Helsinki and Helsinki University Hospital , Helsinki , Finland ;,b Bacteriology and Immunology Department , University of Helsinki and Helsinki University Hospital , Helsinki , Finland ;,c Immunobiology Research Program, Research Programs Unit , University of Helsinki and Helsinki University Hospital , Helsinki , Finland
| | - Hanna Peterson
- d Department of Biosciences and Nutrition , Karolinska Institutet , Stockholm , Sweden
| | - Katja Kivinen
- e Division of Cardiovascular Medicine, University of Cambridge , Cambridge , UK
| | | | - Elina Salmela
- g Molecular Neurology Research Program, Research Programs Unit , University of Helsinki and Helsinki University Hospital , Helsinki , Finland ;,h Folkhälsan Institute of Genetics , Helsinki , Finland
| | - Tuuli Lappalainen
- i New York Genome Center , New York City , NY , USA ;,j Department of Systems Biology , Columbia University , New York City , NY , USA
| | - Paula Maanselkä
- k Institute of Biotechnology , University of Helsinki , Helsinki , Finland
| | - Sanna Heino
- a Medical and Clinical Genetics , University of Helsinki and Helsinki University Hospital , Helsinki , Finland
| | - Sakari Knuutila
- l Department of Pathology , University of Helsinki , Helsinki , Finland
| | - Ayat Sayed
- m Department of Medical Biochemistry, Faculty of Medicine , Assiut University , Assiut , Egypt ;,n School of Molecular Medical Sciences , University of Nottingham , Nottingham , UK
| | - Lucilla Poston
- o Division of Women's Health , King's College London , London , UK
| | - Shaun P Brennecke
- p Department of Maternal-Fetal Medicine , Pregnancy Research Centre and University of Melbourne's Department of Obstetrics and Gynaecology, Royal Women's Hospital , Parkville , Victoria , Australia
| | - Matthew P Johnson
- q South Texas Diabetes and Obesity Institute, School of Medicine , University of Texas Rio Grande Valley , Brownsville , TX , USA
| | - Linda Morgan
- r School of Life Sciences , University of Nottingham , Nottingham , UK
| | - Eric K Moses
- s Faculty of Medicine Dentistry and Health Sciences , The University of Western Australia , Perth , Australia ;,t School of Biomedical Sciences , Faculty of Health Science, Curtin University , Perth , Australia ;,u Centre for Genetic Origins of Health and Disease, Medical Research Foundation , Royal Perth Hospital , Perth , Australia
| | - Juha Kere
- d Department of Biosciences and Nutrition , Karolinska Institutet , Stockholm , Sweden ;,g Molecular Neurology Research Program, Research Programs Unit , University of Helsinki and Helsinki University Hospital , Helsinki , Finland ;,h Folkhälsan Institute of Genetics , Helsinki , Finland
| | - Hannele Laivuori
- a Medical and Clinical Genetics , University of Helsinki and Helsinki University Hospital , Helsinki , Finland ;,v Institute for Molecular Medicine Finland , University of Helsinki , Helsinki , Finland
| |
Collapse
|
22
|
Armengol G, Sarhadi VK, Ghanbari R, Doghaei-Moghaddam M, Ansari R, Sotoudeh M, Puolakkainen P, Kokkola A, Malekzadeh R, Knuutila S. Driver Gene Mutations in Stools of Colorectal Carcinoma Patients Detected by Targeted Next-Generation Sequencing. J Mol Diagn 2016; 18:471-9. [PMID: 27155048 DOI: 10.1016/j.jmoldx.2016.01.008] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2015] [Revised: 11/25/2015] [Accepted: 01/20/2016] [Indexed: 12/13/2022] Open
Abstract
Detection of driver gene mutations in stool DNA represents a promising noninvasive approach for screening colorectal cancer (CRC). Amplicon-based next-generation sequencing (NGS) is a good option to study mutations in many cancer genes simultaneously and from a low amount of DNA. Our aim was to assess the feasibility of identifying mutations in 22 cancer driver genes with Ion Torrent technology in stool DNA from a series of 65 CRC patients. The assay was successful in 80% of stool DNA samples. NGS results showed 83 mutations in cancer driver genes, 29 hotspot and 54 novel mutations. One to five genes were mutated in 75% of cases. TP53, KRAS, FBXW7, and SMAD4 were the top mutated genes, consistent with previous studies. Of samples with mutations, 54% presented concomitant mutations in different genes. Phosphatidylinositol 3-kinase/mitogen-activated protein kinase pathway genes were mutated in 70% of samples, with 58% having alterations in KRAS, NRAS, or BRAF. Because mutations in these genes can compromise the efficacy of epidermal growth factor receptor blockade in CRC patients, identifying mutations that confer resistance to some targeted treatments may be useful to guide therapeutic decisions. In conclusion, the data presented herein show that NGS procedures on stool DNA represent a promising tool to detect genetic mutations that could be used in the future for diagnosis, monitoring, or treating CRC.
Collapse
Affiliation(s)
- Gemma Armengol
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland; Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Autonomous University of Barcelona, Barcelona, Spain
| | - Virinder K Sarhadi
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland
| | - Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | | | - Reza Ansari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Masoud Sotoudeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Pauli Puolakkainen
- Gastrointestinal Clinic, The University Central Hospital of Helsinki, Helsinki, Finland
| | - Arto Kokkola
- Gastrointestinal Clinic, The University Central Hospital of Helsinki, Helsinki, Finland
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran; Sasan Alborz Biomedical Research Center, Masoud Clinic, Tehran, Iran
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, University of Helsinki, Helsinki, Finland.
| |
Collapse
|
23
|
Knuutila S. Mutations by Next Generation Sequencing in Stool DNA from Colorectal Carcinoma Patients – A Literature Review and our Experience with this Methodology. ACTA ACUST UNITED AC 2016. [DOI: 10.6000/1927-7229.2016.05.01.3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022]
|
24
|
Ghanbari R, Mosakhani N, Sarhadi VK, Armengol G, Nouraee N, Mohammadkhani A, Khorrami S, Arefian E, Paryan M, Malekzadeh R, Knuutila S. Simultaneous Underexpression of let-7a-5p and let-7f-5p microRNAs in Plasma and Stool Samples from Early Stage Colorectal Carcinoma. Biomark Cancer 2016; 7:39-48. [PMID: 26793011 PMCID: PMC4711391 DOI: 10.4137/bic.s25252] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/24/2015] [Revised: 09/17/2015] [Accepted: 09/23/2015] [Indexed: 12/23/2022]
Abstract
Colorectal cancer (CRC) is the third most common malignancy and the second most common cause of cancer death worldwide. Early detection of CRC can improve patient survival rates; thus, the identification of noninvasive diagnostic markers is urgently needed. MicroRNAs (miRNAs) have extensive potential to diagnose several diseases, including cancer. In this study, we compared the expression pattern of miRNAs from plasma and stool samples of patients with early stages of CRC (I, II) with that of healthy subjects. We performed miRNA profiling using microarrays on plasma and stool samples of eight patients with CRC and four healthy subjects. Seven miRNAs were found to be underexpressed in both plasma and stool samples of patients with CRC versus healthy subjects. Then, we aimed to verify two out of these seven differentially expressed miRNAs (let-7a-5p and let-7f-5p) by quantitative reverse transcriptase polymerase chain reaction on a larger set of plasma and stool samples of 51 patients with CRC and 26 healthy subjects. We confirmed the results of microarray analysis since their expression was significantly lower in stool and plasma samples of patients with CRC. Moreover, receiver operating characteristic curve analysis demonstrated that fecal let-7f expression levels have significant sensitivity and specificity to distinguish between patients with CRC and healthy subjects. In conclusion, if the results are confirmed in larger series of patients, underexpressed let-7a-5p and let-7f-5p miRNAs in both plasma and stool samples of patients with CRC may serve potentially as noninvasive molecular biomarkers for the early detection of CRC.
Collapse
Affiliation(s)
- Reza Ghanbari
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Mosakhani
- Department of Pathology, Faculty of Medicine, The University of Helsinki, Helsinki, Finland
| | - Virinder K Sarhadi
- Department of Pathology, Faculty of Medicine, The University of Helsinki, Helsinki, Finland
| | - Gemma Armengol
- Department of Pathology, Faculty of Medicine, The University of Helsinki, Helsinki, Finland.; Unit of Biological Anthropology, Department of Animal Biology, Plant Biology and Ecology, Universitat Autònoma de Barcelona, Barcelona, Catalonia, Spain
| | - Nazila Nouraee
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Moddares University, Tehran, Iran
| | - Ashraf Mohammadkhani
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Samaneh Khorrami
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Ehsan Arefian
- Department of Microbiology, School of Biology, College of Science, University of Tehran, Tehran, Iran
| | - Mahdi Paryan
- Research and Development Department, Production and Research Complex, Pasteur Institute of Iran, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sakari Knuutila
- Department of Pathology, Faculty of Medicine, The University of Helsinki, Helsinki, Finland
| |
Collapse
|
25
|
Veija T, Sarhadi VK, Koljonen V, Bohling T, Knuutila S. Hotspot mutations in polyomavirus positive and negative Merkel cell carcinomas. Cancer Genet 2016; 209:30-5. [DOI: 10.1016/j.cancergen.2015.11.006] [Citation(s) in RCA: 20] [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: 07/23/2015] [Revised: 11/19/2015] [Accepted: 11/21/2015] [Indexed: 12/16/2022]
|
26
|
Sarhadi VK, Parkkinen J, Reito A, Nieminen J, Porkka N, Wirtanen T, Laitinen M, Eskelinen A, Knuutila S. Genetic alterations in periprosthetic soft-tissue masses from patients with metal-on-metal hip replacement. Mutat Res 2015; 781:1-6. [PMID: 26355908 DOI: 10.1016/j.mrfmmm.2015.08.006] [Citation(s) in RCA: 9] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2015] [Revised: 07/23/2015] [Accepted: 08/27/2015] [Indexed: 02/06/2023]
Abstract
Adverse soft tissue reactions in patients with metal-on-metal (MoM) hip replacement are associated with cobalt (Co) and chromium (Cr) particles released from the implant. Exposing the patients to long periods of increased metal ions concentrations resulting from the wear of these implants poses an increased risk of genotoxicity/mutagenicity. A variable proportion of patients develop periprosthetic soft-tissue masses or pseudotumors at the site of the implant. There is a concern that exposure to increased metal ions could increase the risk of cancer. In order to investigate whether the periprosthetic soft-tissue mass harbours any cancer- related genetic alterations, we studied DNA isolated from periprosthetic tissues of 20 patients with MoM hip replacement, for copy number alterations and mutations in hotspot regions of 50 cancer genes using aCGH and amplicon-based next generation sequencing. Our results showed copy number gains at 12q14.3 and 21q21.1in tumour from patient diagnosed with liposarcoma. Copy number alterations in periprosthetic tissues were seen in three other patients, one had a region of gain at 9q24.1 affecting JAK2 and INSL6, and two patients had region of gain at 6p21.1, affecting RUNX2. Mutation analysis showed V1578del mutation in NOTCH1 in two patients. The copy number alterations and mutations seen in periprosthetic soft-tissue masses are earlier reported in either haematological malignancies or in osteoblast related bone dysplasia. The presence of genetic anomalies was associated with longer in-situ time of the implant. Our findings warrant the need of similar studies in larger patient cohorts to evaluate the risk of development of neoplastic alterations in periprosthetic tissues of patients with MoM hip replacement.
Collapse
Affiliation(s)
- Virinder Kaur Sarhadi
- University of Helsinki, Faculty of Medicine, Department of Pathology, Helsinki, Finland
| | - Jyrki Parkkinen
- Coxa Hospital for Joint Replacement, Tampere, Finland; Department of Pathology, FIMLAB Laboratories, Tampere, Finland
| | - Aleksi Reito
- Coxa Hospital for Joint Replacement, Tampere, Finland
| | | | - Noora Porkka
- University of Helsinki, Faculty of Medicine, Department of Pathology, Helsinki, Finland
| | - Tiina Wirtanen
- University of Helsinki, Faculty of Medicine, Department of Pathology, Helsinki, Finland; HUSLAB, Department of Pathology, Helsinki University Central Hospital, Helsinki, Finland
| | | | | | - Sakari Knuutila
- University of Helsinki, Faculty of Medicine, Department of Pathology, Helsinki, Finland.
| |
Collapse
|
27
|
Brunelli M, Nottegar A, Bogina G, Caliò A, Cima L, Eccher A, Vicentini C, Marcolini L, Scarpa A, Pedron S, Brunello E, Knuutila S, Sapino A, Marchiò C, Bria E, Molino A, Carbognin L, Tortora G, Jasani B, Miller K, Merdol I, Zanatta L, Laurino L, Wirtanen T, Zamboni G, Marconi M, Chilosi M, Manfrin E, Martignoni G, Bonetti F. Monosomy of chromosome 17 in breast cancer during interpretation of HER2 gene amplification. Am J Cancer Res 2015; 5:2212-2221. [PMID: 26328251 PMCID: PMC4548332] [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] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2015] [Accepted: 06/11/2015] [Indexed: 06/04/2023] Open
Abstract
Monosomy of chromosome 17 may affect the assessment of HER2 amplification. Notably, the prevalence ranges from 1% up to 49% due to lack of consensus in recognition. We sought to investigate the impact of monosomy of chromosome 17 to interpretation of HER2 gene status. 201 breast carcinoma were reviewed for HER2 gene amplification and chromosome 17 status. FISH analysis was performed by using double probes (LSI/CEP). Absolute gene copy number was also scored per each probe. HER2 FISH test was repeated on serial tissue sections, ranging in thickness from 3 to 20 µm. Ratio was scored and subsequently corrected by monosomy after gold control test using the aCGH method to overcome false interpretation due to artefactual nuclear truncation. HER2 immunotests was performed on all cases. 26/201 cases were amplified (13%). Single signals per CEP17 were revealed in 7/201 (3.5%) cases. Five out of 7 cases appeared monosomic with aCGH (overall, 5/201, 2.5%) and evidenced single signals in >60% of nuclei after second-look on FISH when matching both techniques. Among 5, one case showed amplification with a pattern 7/1 (HER2/CEP17>2) of copies (3+ at immunotest); three cases revealed single signals per both probes (LSI/CEP=1) and one case revealed a 3:1 ratio; all last 4 cases showed 0/1+ immunoscore. We concluded that: 1) monosomy of chromosome 17 may be observed in 2.5% of breast carcinoma; 2) monosomy of chromosome 17 due to biological reasons rather than nuclear truncation was observed when using the cut-off of 60% of nuclei harboring single signals; 3) the skewing of the ratio due to single centromeric 17 probe may lead to false positive evaluation; 4) breast carcinomas showing a 3:1 ratio (HER2/CEP17) usually show negative 0/1+ immunoscore and <6 gene copy number at FISH.
Collapse
Affiliation(s)
- Matteo Brunelli
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Alessia Nottegar
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Giuseppe Bogina
- Anatomic Pathology, Sacro Cuore Don Calabria HospitalNegrar, Italy
| | - Anna Caliò
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Luca Cima
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Albino Eccher
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | | | - Lisa Marcolini
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Aldo Scarpa
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
- ARC-NET Applied Research Centre, University of VeronaItaly
| | - Serena Pedron
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Eleonora Brunello
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Sakari Knuutila
- Department of Pathology, Laboratory of Molecular Cytogenetic, University of HelsinkiFinland
| | - Anna Sapino
- Department of Medical Sciences, Anatomic Pathology, University and Hospital TrustTurin, Italy
| | - Caterina Marchiò
- Department of Medical Sciences, Anatomic Pathology, University and Hospital TrustTurin, Italy
| | - Emilio Bria
- Medical Oncology, University and Hospital TrustVerona, Italy
| | | | - Luisa Carbognin
- Medical Oncology, University and Hospital TrustVerona, Italy
| | | | - Bharat Jasani
- Institute of Cancer & Genetics, Pathology, Cardiff UniversityUnited Kingdom
| | - Keith Miller
- UK NEQAS, University College of LondonUnited Kingdom
| | | | - Lucia Zanatta
- Anatomic Pathology, S. Maria di Ca’ Foncello HospitalTreviso, Italy
| | - Licia Laurino
- Anatomic Pathology, S. Maria di Ca’ Foncello HospitalTreviso, Italy
| | - Tiina Wirtanen
- Department of Pathology, Laboratory of Molecular Cytogenetic, University of HelsinkiFinland
- Department of Pathology, HUSLab, University Central HospitalHelsinki, Finland
| | - Giuseppe Zamboni
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
- Anatomic Pathology, Sacro Cuore Don Calabria HospitalNegrar, Italy
| | - Marcella Marconi
- Anatomic Pathology, Sacro Cuore Don Calabria HospitalNegrar, Italy
| | - Marco Chilosi
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Erminia Manfrin
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Guido Martignoni
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| | - Franco Bonetti
- Department of Pathology and Diagnostic, Anatomic Pathology, University and Hospital TrustVerona, Italy
| |
Collapse
|
28
|
Ghanbari R, Mosakhani N, Asadi J, Nouraee N, Mowla SJ, Yazdani Y, Mohamadkhani A, Poustchi H, Knuutila S, Malekzadeh R. Downregulation of Plasma MiR-142-3p and MiR-26a-5p in Patients With Colorectal Carcinoma. Iran J Cancer Prev 2015; 8:e2329. [PMID: 26413249 PMCID: PMC4581368 DOI: 10.17795/ijcp2329] [Citation(s) in RCA: 45] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/21/2014] [Revised: 11/05/2014] [Accepted: 11/12/2014] [Indexed: 12/21/2022]
Abstract
Background: Colorectal cancer is one of the most commonly diagnosed cancers and cancer- related death worldwide. Identification of new specific biomarkers could be helpful to detection of this malignancy. Altered plasma microRNA expression has been identified in many cancers, including colorectal cancer. Objectives: The main objective of this study was to identify the circulating microRNAs with the most expression changes in colorectal cancer patients compared with neoplasm free healthy individuals. Materials and Methods: MicroRNA expression profiling was performed on plasma samples of 37 colorectal cancer patients and 8 normal subjects using microRNA microarray. Quantitative real-time reverse transcription polymerase chain reaction was used to validate the two selected altered microR NAs. Plasma samples from 61 colorectal cancer patients and 24 normal subjects were used in our validation study. Results: In profiling study we found a panel of six plasma microRNAs with significant downregulation. MicroRNA-142-3p and microRNA-26a-5p were selected and validated by polymerase chain reaction. Our results demonstrated that expression levels of plasma microRNA-142-3p and microRNA-26a-5p were significantly downregulated in patients with colorectal cancer when compared to control group. Conclusions: Our findings suggest that downregulation of plasma microRNA-142-3p and microRNA-26a-5p might serve as novel noninvasive biomarkers in the diagnosis of colorectal cancer, although more studies are needed to highlight the theoretical strengths.
Collapse
Affiliation(s)
- Reza Ghanbari
- Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, IR Iran ; Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Neda Mosakhani
- Department of Pathology, Haartman Institute, Helsinki University, Helsinki, Finland
| | - Jahanbakhsh Asadi
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
| | - Nazila Nouraee
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Moddares University, Tehran, IR Iran
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Moddares University, Tehran, IR Iran
| | - Yaghoub Yazdani
- Infectious Disease Research Center, Golestan University of Medical Sciences, Gorgan, IR Iran
| | - Ashraf Mohamadkhani
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Hossein Poustchi
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, IR Iran
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute, Helsinki University, Helsinki, Finland
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, IR Iran
| |
Collapse
|
29
|
Ghanbari R, Mosakhani N, Asadi J, Nouraee N, Mowla SJ, Poustchi H, Malekzadeh R, Knuutila S. Decreased expression of fecal miR-4478 and miR-1295b-3p in early-stage colorectal cancer. Cancer Biomark 2015; 15:189-95. [DOI: 10.3233/cbm-140453] [Citation(s) in RCA: 24] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
Affiliation(s)
- Reza Ghanbari
- Faculty of Advanced Medical Technologies, Golestan University of Medical Sciences, Gorgan, Iran
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Neda Mosakhani
- Department of Pathology, Haartman Institute, Helsinki University, Helsinki, Finland
| | - Jahanbakhsh Asadi
- Metabolic Disorders Research Center, Golestan University of Medical Sciences, Gorgan, Iran
| | - Nazila Nouraee
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Seyed Javad Mowla
- Department of Molecular Genetics, Faculty of Biological Sciences, Tarbiat Modares University, Tehran, Iran
| | - Hossein} Poustchi
- Liver and Pancreatobiliary Disease Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Reza Malekzadeh
- Digestive Oncology Research Center, Digestive Diseases Research Institute, Tehran University of Medical Sciences, Tehran, Iran
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute, Helsinki University, Helsinki, Finland
| |
Collapse
|
30
|
Söderström M, Dalin-Hirvonen N, Mattila K, Knuutila S, Kallajoki M. [Diagnosis of soft tissue tumors--multidisciplinary collaboration]. Duodecim 2015; 131:769-780. [PMID: 26237892] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [MESH Headings] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
The number of soft tissue sarcomas found in Finland yearly is around 200 cases. Benign soft tissue tumors are common. The patients having a tumor with a deep location in the tissue or a large superficial tumor should be readily referred for imaging studies and consultations with the sarcoma teams of university hospitals. The diagnosis of sarcoma is based on medical history, clinical examination, imaging, examination of a biopsy, and frequently also on molecular genetic analyses. In imaging, the best resolution is provided by MRI. Targeting of the biopsy is an essential part of imaging. Gradus is the most important histology-based factor affecting the prognosis and treatment of the tumor.
Collapse
|
31
|
Siggberg L, Ala-Mello S, Linnankivi T, Avela K, Scheinin I, Kristiansson K, Lahermo P, Hietala M, Metsähonkala L, Kuusinen E, Laaksonen M, Saarela J, Knuutila S. Erratum to: High-resolution SNP array analysis of patients with developmental disorder and normal array CGH result. BMC Med Genet 2014; 15:124. [PMID: 25928284 PMCID: PMC4429685 DOI: 10.1186/s12881-014-0124-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Affiliation(s)
- Linda Siggberg
- Department of Pathology, Haartman Institute, University of Helsinki, and Laboratory of Helsinki and Uusimaa University Hospital, Helsinki, Finland.
| | - Sirpa Ala-Mello
- Rinnekoti Foundation, Rehabilitation Home for Children, Espoo, Finland.
| | - Tarja Linnankivi
- Department of Pediatric Neurology, Helsinki University Central Hospital, Helsinki, Finland.
| | - Kristiina Avela
- Department of Medical Genetics, Väestöliitto, The Family Federation of Finland, Helsinki, Finland.
| | - Ilari Scheinin
- Department of Pathology, Haartman Institute, University of Helsinki, and Laboratory of Helsinki and Uusimaa University Hospital, Helsinki, Finland. .,Department of Pathology, VU University Medical Center, Amsterdam, The Netherlands. .,Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland.
| | - Kati Kristiansson
- Public Health Genomics Unit, Department of Chronic Disease Prevention, National Institute for Health and Welfare, Helsinki, Finland. .,Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland.
| | - Päivi Lahermo
- Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland.
| | - Marja Hietala
- Department of Clinical Genetics, Turku University Hospital and Department of Medical Biochemistry and Genetics, University of Turku, Turku, Finland.
| | - Liisa Metsähonkala
- Department of Pediatric Neurology, Helsinki University Central Hospital, Helsinki, Finland.
| | - Esa Kuusinen
- Department of Pediatrics, Satakunta Hospital District, Pori, Finland.
| | - Maarit Laaksonen
- Population Health Unit, Department of Health, Functional Capacity and Welfare, National Institute for Health and Welfare, P.O. Box 21, 00014, Helsinki, Finland.
| | - Janna Saarela
- Institute for Molecular Medicine Finland FIMM, University Helsinki, Helsinki, Finland.
| | - Sakari Knuutila
- Department of Pathology, Haartman Institute, University of Helsinki, and Laboratory of Helsinki and Uusimaa University Hospital, Helsinki, Finland.
| |
Collapse
|
32
|
Pazzaglia L, Guled M, Borze I, Benassi MS, Picci P, Knuutila S. Abstract 5196: Different miRNAs expression in leiomyosarcoma and undifferentiated pleomorphic sarcoma. Cancer Res 2014. [DOI: 10.1158/1538-7445.am2014-5196] [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
Rare and highly aggressive adult soft tissue sarcomas, leiomyosarcoma (LMS) and undifferentiated pleomorphic sarcoma (UPS), contain complex genomics characterized by a multitude of rearrangements, amplifications and deletions. Since differential diagnosis between the two sarcoma histotypes continues to remain a challenge, we attempted to identify a specific signature useful for improving the differential diagnosis, and we performed miRNA profiling on series of LMS and UPS samples stored at Rizzoli biobank. First, we investigated the different miRNA expression profile in 20 primary sarcoma samples, 10 high-grade LMS and 10 UPS, MFH-like, using miRNA array technique. The top 5 differentially expressed (p<0.01) miRNAs (miR-199b-5p, miR-320a, miR-199a-3p, miR-126, miR-22) were validated by RT-PCR on a series of further 27 UPS and 21 LMS. Confirming our microarray data, an higher expression of miR-199-5p and a lower expression of miR-320a was seen in UPS when compared to LMS. To evaluate the potential role of the above selected miRNAs, the gene targets recognized by three different target prediction databases (miRBase, TargetScan , miRanda) were combined with a list of LMS- and UPS-associated genes reported in literature. From an integrated analysis, IMP3, ROR2, MDM2, CDK4, and UPA genes were identified. By immunohistochemistry analysis, most of them showed strong protein expression in LMS group. Our data suggest a potential role of miR-320a and miR-199-5p in LMS and UPS development and expand our knowledge about these complex sarcoma histotypes. Association analysis between expression and chromosomal locations of miRNAs are ongoing to identify chromosomal regions involved in these tumors.
Citation Format: Laura Pazzaglia, Mohamed Guled, Ioana Borze, Maria Serena Benassi, Piero Picci, Sakari Knuutila. Different miRNAs expression in leiomyosarcoma and undifferentiated pleomorphic sarcoma. [abstract]. In: Proceedings of the 105th Annual Meeting of the American Association for Cancer Research; 2014 Apr 5-9; San Diego, CA. Philadelphia (PA): AACR; Cancer Res 2014;74(19 Suppl):Abstract nr 5196. doi:10.1158/1538-7445.AM2014-5196
Collapse
Affiliation(s)
| | - Mohamed Guled
- 2University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | - Ioana Borze
- 2University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | | | - Piero Picci
- 1Istituto Ortopedico Rizzoli, Bologna, Italy
| | - Sakari Knuutila
- 2University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| |
Collapse
|
33
|
Vanhapiha N, Knuutila S, Vettenranta K, Lohi O. Burkitt lymphoma and Ewing sarcoma in a child with Williams syndrome. Pediatr Blood Cancer 2014; 61:1877-9. [PMID: 24753445 DOI: 10.1002/pbc.25055] [Citation(s) in RCA: 10] [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] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 01/02/2014] [Accepted: 03/10/2014] [Indexed: 11/08/2022]
Abstract
Williams syndrome (WS) is a relatively rare multisystem neurodevelopmental disorder caused by a hemizygous deletion of contiguous genes on chromosome 7q11.23. Although WS does not predispose carriers to cancers, alterations of chromosome 7 are common in several human neoplasms. We report here a patient with WS and two different cancers, Burkitt lymphoma and Ewing sarcoma. Array-CGH analysis of the patient blood revealed a constitutive 1.4 million base pair deletion at 7q11.23, compatible with WS diagnosis.
Collapse
Affiliation(s)
- Nelli Vanhapiha
- Tampere Center for Child Health Research, University of Tampere Medical School and Tampere University Hospital, Tampere, Finland
| | | | | | | |
Collapse
|
34
|
Massari F, Ciccarese C, Knuutila S, Russa FL, Bimbatti D, Modena A, Zampini C, Porcaro A, Sava T, Artibani W, Martignoni G, Brunelli M, Tortora G. Loss of Chromosomes 9P and 14Q: Re-Profiling Metastatic Tissue for Re-Targeting Patients with Metastatic Renal Cell Carcinoma. Ann Oncol 2014. [DOI: 10.1093/annonc/mdu337.13] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
|
35
|
Merkkiniemi K, Kero M, Mäki-Nevala S, Sarhadi V, Tikkanen M, Wirtanen T, Rönty M, Knuuttila A, Knuutila S. 672: ALK fusion in a cohort of 469 Finnish patients with non-small cell lung cancer. Eur J Cancer 2014. [DOI: 10.1016/s0959-8049(14)50592-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
|
36
|
Tuononen K, Kero M, Mäki-Nevala S, Sarhadi VK, Tikkanen M, Wirtanen T, Rönty M, Knuuttila A, Knuutila S. ALK fusion and its association with other driver gene mutations in Finnish non-small cell lung cancer patients. Genes Chromosomes Cancer 2014; 53:895-901. [PMID: 24942490 DOI: 10.1002/gcc.22198] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/03/2014] [Revised: 06/08/2014] [Accepted: 06/10/2014] [Indexed: 01/29/2023] Open
Abstract
Screening of anaplastic lymphoma tyrosine kinase (ALK) gene fusions in non-small cell lung cancer (NSCLC) patients enables the identification of the patients likely to benefit from ALK-targeted therapy. Our aim was to assess the prevalence of ALK fusion in Finnish NSCLC patients, which has not been reported earlier, and to study the presence of ALK fusion in relation to clinicopathological characteristics and other driver gene mutations. A total of 469 formalin-fixed paraffin-embedded tumor tissue specimens from Finnish NSCLC patients were screened for ALK fusion by immunohistochemistry (IHC). For confirmation of IHC results, fluorescence in situ hybridization (FISH) was conducted for 171 specimens. Next-generation sequencing was performed for all ALK-positive specimens to characterize the association of ALK fusion with mutations in targeted regions of 22 driver genes. Of the 469 tumors screened, 11 (2.3%) harbored an ALK fusion, including nine adenocarcinomas and two large cell carcinomas. The IHC results for all 11 ALK-positive and 160 random ALK-negative specimens were confirmed by FISH. ALK fusion was significantly associated with never/ex-light smoking history (P<0.001) and younger age (P=0.004). Seven ALK-positive tumors showed additional mutations; three in MET, one in MET and CTNNB1, two in TP53, and one in PIK3CA. Our results show that ALK fusion is an infrequent alteration in Finnish NSCLC patients. Although the majority of ALK-positive cases were adenocarcinomas, the fusion was also seen in large cell carcinomas. Further studies are needed to elucidate the clinical significance of the coexistence of ALK fusion with MET, TP53, CTNNB1, and PIK3CA mutations.
Collapse
Affiliation(s)
- Katja Tuononen
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | |
Collapse
|
37
|
Guled M, Pazzaglia L, Borze I, Mosakhani N, Novello C, Benassi MS, Knuutila S. Differentiating soft tissue leiomyosarcoma and undifferentiated pleomorphic sarcoma: A miRNA analysis. Genes Chromosomes Cancer 2014; 53:693-702. [PMID: 24771630 DOI: 10.1002/gcc.22179] [Citation(s) in RCA: 30] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2013] [Revised: 04/05/2014] [Accepted: 04/07/2014] [Indexed: 01/08/2023] Open
Abstract
The rare and highly aggressive adult soft tissue sarcomas leiomyosarcoma (LMS) and undifferentiated pleomorphic sarcoma (UPS) contain complex genomes characterized by a multitude of rearrangements, amplifications, and deletions. Differential diagnosis remains a challenge. MicroRNA (miRNA) profiling was conducted on a series of LMS and UPS samples to initially investigate the differential expression and to identify specific signatures useful for improving the differential diagnosis. Initially, 10 high-grade LMS and 10 high-grade UPS were profiled with a miRNA microarray. Two cultured human mesenchymal stem cell samples were used as controls. 38 and 46 miRNAs classified UPS and LMS samples, respectively, into separate groups compared to control samples. When comparing the two profiles, miR-199b-5p, miR-320a, miR-199a-3p, miR-126, miR-22 were differentially expressed. These were validated by RT-PCR on a further series of 27 UPS and 21 LMS for a total of 68 cases. The levels of miR-199-5p and miR-320a, in particular, confirmed the microarray data, the former highly expressed in UPS and the latter in LMS. Immunohistochemistry was performed on all 68 cases to confirm original diagnosis. Recently reported LMS- and UPS-associated genes were correlated with miRNA targets based on target algorithms of three databases. Several genes including IMP3, ROR2, MDM2, CDK4, and UPA, are targets of differentially expressed miRNAs. We identified miRNA expression patterns in LMS and UPS, linking them to chromosomal regions and mRNA targets known to be involved in tumor development/progression of LMS and UPS.
Collapse
Affiliation(s)
- Mohamed Guled
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | | | | | | | | | | | | |
Collapse
|
38
|
Manceau G, Imbeaud S, Thiébaut R, Liébaert F, Fontaine K, Rousseau F, Génin B, Le Corre D, Didelot A, Vincent M, Bachet JB, Chibaudel B, Bouché O, Landi B, Bibeau F, Leroy K, Penault-Llorca F, Van Laethem JL, Demetter P, Tejpar S, Rossi S, Mosakhani N, Osterlund P, Ristamäki R, Sarhadi V, Knuutila S, Boige V, André T, Laurent-Puig P. Hsa-miR-31-3p expression is linked to progression-free survival in patients with KRAS wild-type metastatic colorectal cancer treated with anti-EGFR therapy. Clin Cancer Res 2014; 20:3338-47. [PMID: 24771647 DOI: 10.1158/1078-0432.ccr-13-2750] [Citation(s) in RCA: 79] [Impact Index Per Article: 7.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/12/2022]
Abstract
PURPOSE To identify microRNAs (miRNA) that predict response to anti-EGFR antibodies in patients with wild-type KRAS metastatic colorectal cancer (mCRC). EXPERIMENTAL DESIGN miRNA profiling was performed in a training set of 87 patients with mCRC refractory to chemotherapy treated with anti-EGFR antibodies. This included 33 fresh-frozen (FF) and 35 formalin-fixed paraffin-embedded (FFPE) samples retrospectively collected and 19 prospectively collected FF samples. An independent validation cohort consisting of 19 FF and 26 FFPE prospectively collected samples from patients with mCRC treated with anti-EGFR antibodies was used to confirm our findings. RESULTS After screening the expression of 1,145 miRNAs in FF samples from the training set, we identified that hsa-miR-31-3p expression level was significantly associated with progression-free survival (PFS). Statistical models based on miRNA expression discriminated between high and low risk of progression for both FF and FFPE samples. These models were confirmed in the validation cohort for both FF [HR, 4.1; 95% confidence interval (CI), 1.1-15.3; P < 0.04] and FFPE samples (HR, 2.44; 95% CI, 1.1-5.4; P = 0.028). The percentage of variation of RECIST criteria in the validation series was significantly associated with the expression level of hsa-miR-31-3p (r(2) = 0.49; P = 0.0035) and risk status determined by hsa-miR-31-3p expression level (P = 0.02, Kruskal-Wallis rank test). Nomograms were built and validated to predict PFS-depending on hsa-miR-31-3p expression level. Following in vitro studies, we identified 47 genes regulated by hsa-miR-31-3p. CONCLUSION Hsa-miR-31-3p seems to be a new mCRC biomarker whose expression level allows for the identification of patients with wild-type KRAS mCRC who are more likely to respond to anti-EGFR therapy.
Collapse
Affiliation(s)
- Gilles Manceau
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, FinlandAuthors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpit
| | - Sandrine Imbeaud
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Raphaële Thiébaut
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - François Liébaert
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Karine Fontaine
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Francis Rousseau
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Bérengère Génin
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Delphine Le Corre
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Audrey Didelot
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Marc Vincent
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Jean-Baptiste Bachet
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Benoist Chibaudel
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Olivier Bouché
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Bruno Landi
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Frédéric Bibeau
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Karen Leroy
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Frédérique Penault-Llorca
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Jean-Luc Van Laethem
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Pieter Demetter
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Sabine Tejpar
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Simona Rossi
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Neda Mosakhani
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Pia Osterlund
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Raija Ristamäki
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Virinder Sarhadi
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Sakari Knuutila
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, FinlandAuthors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpit
| | - Valérie Boige
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, FinlandAuthors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpit
| | - Thierry André
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, Finland
| | - Pierre Laurent-Puig
- Authors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Saint-Antoine; Assistance Publique-Hôpitaux de Paris, Hôpital Européen Georges Pompidou, service d'Hépato-Gastro-Entérologie et d'Oncologie Digestive; Université Paris-Est Créteil; Assistance Publique-Hôpitaux de Paris, Hôpital Henri Mondor, Créteil; Department of Medicine, Institut Gustave Roussy, Villejuif; and Department of Biology, Assistance Publique-Hôpitaux de Paris, European Georges Pompidou, Paris; Université de Reims Champagne-Ardenne; Centre Hospitalier Universitaire de Reims, Reims; Service d'Anatomo-Pathologie, Centre Val d'Aurelle Paul-Lamarque, Montpellier; Université Clermont-Ferrand, Centre Jean Perrin, Clermont-Ferrand, France; Department of Gastroenterology, GI Cancer Unit; Department of Pathological Anatomy, Erasme University Hospital, Brussels; Digestive Oncology Unit, University Hospital Gasthuisberg, Leuven, Belgium; Bioinformatics Core Facility, Swiss Institute of Bioinformatics, Lausanne, Switzerland; Haartman Institute, University of Helsinki; Department of Oncology, Helsinki University Central Hospital and Helsinki University; HUSLAB, Department of Pathology and Genetic Laboratory, Helsinki; and Department of Oncology and Radiotherapy, Turku University Hospital, Turku, FinlandAuthors' Affiliations: Université Paris Sorbonne Cité; INSERM UMR-S775 Bases Moléculaires de la réponse aux xénobiotiques; INSERM UMR-S674 Genomique Fonctionnelle des Tumeurs; Integragen S.A., Evry; Université Pierre et Marie Curie; Assistance Publique-Hôpitaux de Paris, Hôpital Pitié Salpétrière; Université Pierre et Marie Curie; Assistance Publique-Hôpit
| |
Collapse
|
39
|
Sahi H, Savola S, Sihto H, Koljonen V, Bohling T, Knuutila S. RB1 gene in Merkel cell carcinoma: hypermethylation in all tumors and concurrent heterozygous deletions in the polyomavirus-negative subgroup. APMIS 2014; 122:1157-66. [PMID: 24735260 DOI: 10.1111/apm.12274] [Citation(s) in RCA: 23] [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] [Subscribe] [Scholar Register] [Received: 11/04/2013] [Accepted: 02/25/2014] [Indexed: 01/04/2023]
Abstract
Sequestration of the tumor suppressor retinoblastoma protein (RB) by the Merkel cell polyomavirus (MCV) is a crucial step in the pathogenesis of Merkel cell carcinoma (MCC). RB expression is frequently lost, particularly in MCV-negative MCC tumors, through yet unknown mechanisms. We compared the genomic copy number changes of 13 MCV-positive and 13 -negative MCC tumors by array comparative genomic hybridization. The analysis revealed increased genomic instability, amplification of 1p34.3-1p34.2, and losses of 11p in the absence of MCV infection. Deletions of the RB1 locus were also detected at high rates in MCV-negative tumors. None of the tumors with heterozygous RB1 losses expressed RB in immunohistochemistry. RB1 promoter hypermethylation was studied with a methylation-specific multiplex ligation-dependent probe amplification technique. The RB1 promoter was methylated in all tumor specimens at CpG islands located close to the ATG start codon, albeit at low levels. The pattern of hypermethylation was similar in all MCC samples, despite RB expression, survival or MCV status. In conclusion, the frequent heterozygous losses of the RB1 locus could partly explain the decreased RB expression in MCV-negative MCC tumors, although the effects of RB1 mutations, coinciding promoter hypermethylation and, for example, miRNA regulation, cannot be excluded.
Collapse
Affiliation(s)
- Helka Sahi
- Department of Pathology, Helsinki University and HUSLAB, Helsinki, Finland; Department of Plastic Surgery, Helsinki University Hospital, Helsinki, Finland
| | | | | | | | | | | |
Collapse
|
40
|
Sarhadi VK, Lahti L, Scheinin I, Ellonen P, Kettunen E, Serra M, Scotlandi K, Picci P, Knuutila S. Copy number alterations and neoplasia-specific mutations inMELK,PDCD1LG2, TLN1, andPAX5at 9p in different neoplasias. Genes Chromosomes Cancer 2014; 53:579-88. [DOI: 10.1002/gcc.22168] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2013] [Accepted: 03/09/2014] [Indexed: 12/16/2022] Open
Affiliation(s)
- Virinder Kaur Sarhadi
- Department of Pathology; Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital; Helsinki Finland
| | - Leo Lahti
- Department of Veterinary Bioscience; University of Helsinki, Finland and Laboratory of Microbiology, Wageningen University; The Netherlands
| | - Ilari Scheinin
- Department of Pathology; Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital; Helsinki Finland
- Department of Pathology; VU University Medical Center; Amsterdam The Netherlands
| | - Pekka Ellonen
- Institute for Molecular Medicine Finland, University of Helsinki; Biomedicum Helsinki 2U Helsinki Finland
| | - Eeva Kettunen
- Health and Work Ability; Finnish Institute of Occupational Health; Helsinki Finland
| | - Massimo Serra
- Laboratory of Experimental Oncology; Orthopaedic Rizzoli Institute; Bologna Italy
| | - Katia Scotlandi
- Laboratory of Experimental Oncology; Orthopaedic Rizzoli Institute; Bologna Italy
| | - Piero Picci
- Laboratory of Experimental Oncology; Orthopaedic Rizzoli Institute; Bologna Italy
| | - Sakari Knuutila
- Department of Pathology; Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital; Helsinki Finland
| |
Collapse
|
41
|
Mäki-Nevala S, Kaur Sarhadi V, Tuononen K, Lagström S, Ellonen P, Rönty M, Wirtanen A, Knuuttila A, Knuutila S. Mutated ephrin receptor genes in non-small cell lung carcinoma and their occurrence with driver mutations-targeted resequencing study on formalin-fixed, paraffin-embedded tumor material of 81 patients. Genes Chromosomes Cancer 2013; 52:1141-9. [PMID: 24123310 DOI: 10.1002/gcc.22109] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2013] [Accepted: 08/13/2013] [Indexed: 01/29/2023] Open
Abstract
Non-small cell lung carcinoma (NSCLC) is the most common subtype of lung cancer. The oncogenic potential of receptor tyrosine kinases (RTKs) is widely known and they are potential targets for tailored therapy. Ephrin receptors (Ephs) form the largest group of RTKs. Nevertheless, Ephs are not widely studied in NSCLC so far. The aim of our study was to investigate novel mutations of Eph genes (EPHA1-8, EPHB1-4, EPHB6) and their association with clinically relevant mutations in BRAF, EML4-ALK, EGFR, INSR, KDR, KRAS, MET, PDGFRA, PDGFRB, PIK3, PTEN, RET, and TP53 in NSCLC patients. Targeted resequencing was conducted on 81 formalin-fixed, paraffin-embedded NSCLC tumor specimens. We analyzed missense and nonsense mutations harbored in the coding regions of the selected genes. We found 18 novel mutations of Ephs in 20% (16 of 81) of the patients. Nearly half of these mutations occurred in the protein kinase domain. The mutations were not mutually exclusive with other clinically relevant mutations. Our study shows that Ephs are frequently mutated in NSCLC patients, and occur together with other known mutations relevant to the pathogenicity of NSCLC.
Collapse
Affiliation(s)
- Satu Mäki-Nevala
- Department of Pathology, Haartman Institute, University of Helsinki, Finland
| | | | | | | | | | | | | | | | | |
Collapse
|
42
|
Catrina Ene AM, Borze I, Guled M, Costache M, Leen G, Sajin M, Ionica E, Chitu A, Knuutila S. MicroRNA expression profiles in Kaposi's sarcoma. Pathol Oncol Res 2013; 20:153-9. [PMID: 24027049 DOI: 10.1007/s12253-013-9678-1] [Citation(s) in RCA: 32] [Impact Index Per Article: 2.9] [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: 06/29/2012] [Accepted: 07/18/2013] [Indexed: 12/15/2022]
Abstract
Kaposi's sarcoma (KS) is a mesenchymal tumor, caused by Human herpesvirus 8 (HHV8) with molecular and cytogenetic changes poorly understood. To gain further insight on the underlying molecular changes in KS, we performed microRNA (miRNA) microarray analysis of 17 Kaposi's sarcoma specimens. Three normal skin specimens were used as controls. The most significant differentially expressed miRNA were confirmed by quantitative reverse transcriptase polymerase chain reaction (RT-PCR). We detected in KS versus normal skin 185 differentially expressed miRNAs, 76 were upregulated and 109 were downregulated. The most significantly downregulated miRNAs were miR-99a, miR-200 family, miR-199b-5p, miR-100 and miR-335, whereas kshv-miR-K12-4-3p, kshv-miR-K12-1, kshv-miR-K12-2, kshv-miR-K12-4-5p and kshv-miR-K12-8 were significantly upregulated. High expression levels of kshv-miR-K12-1 (p = 0.004) and kshv-miR-K12-4-3p (p = 0.001) was confirmed by RT-PCR. The predicted target genes for differentially expressed miRNAs included genes which are involved in a variety of cellular processes such as angiogenesis (i.e. THBS1) and apoptosis (i.e. CASP3, MCL1), suggesting a role for these miRNAs in Kaposi's sarcoma pathogenesis.
Collapse
Affiliation(s)
- Ana Maria Catrina Ene
- Department of Biochemistry and Molecular Biology, Faculty of Biology, University of Bucharest, 050095, Bucharest, Romania
| | | | | | | | | | | | | | | | | |
Collapse
|
43
|
Sarhadi VK, Lahti L, Scheinin I, Tyybäkinoja A, Savola S, Usvasalo A, Räty R, Elonen E, Ellonen P, Saarinen-Pihkala UM, Knuutila S. Targeted resequencing of 9p in acute lymphoblastic leukemia yields concordant results with array CGH and reveals novel genomic alterations. Genomics 2013; 102:182-8. [DOI: 10.1016/j.ygeno.2013.01.001] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/25/2012] [Revised: 01/07/2013] [Accepted: 01/08/2013] [Indexed: 11/16/2022]
|
44
|
Larramendy ML, Kovanen PE, Knuutila S. MAC (Morphology, Antibody, Chromosomes) Method for Study of Cell Proliferation in Unfractionated Human Hematopoietic Cell Cultures. J Histotechnol 2013. [DOI: 10.1179/his.1992.15.1.31] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/31/2022]
|
45
|
Mosakhani N, Mustjoki S, Knuutila S. Down-regulation of miR-181c in imatinib-resistant chronic myeloid leukemia. Mol Cytogenet 2013; 6:27. [PMID: 23866735 PMCID: PMC3751646 DOI: 10.1186/1755-8166-6-27] [Citation(s) in RCA: 27] [Impact Index Per Article: 2.5] [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: 04/17/2013] [Accepted: 06/04/2013] [Indexed: 12/21/2022] Open
Abstract
The association of microRNA alterations with progression and treatment outcome has been revealed in different types of cancers. To find miRNAs involved in imatinib response we performed miRNA microarray followed by RT-qPCR verification of 9 available diagnostic bone marrow core biopsies from 9 CML patients including 4 imatinib-resistant and 5 imatinib-responder patients. Only one differentially expressed miRNA, miR-181c, was found when the imatinib-resistant group was compared with imatinib-responders. Significant down-regulation of miR-181c in imatinib-resistant versus imatinib-responders was confirmed by qRT-PCR. Some miR-181c target genes such as PBX3, HSP90B1, NMT2 and RAD21 have been associated with drug response.
Collapse
Affiliation(s)
- Neda Mosakhani
- Department of Pathology, Haartman Institute, and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland.
| | | | | |
Collapse
|
46
|
Mosakhani N, Räty R, Tyybäkinoja A, Karjalainen-Lindsberg ML, Elonen E, Knuutila S. MicroRNA profiling in chemoresistant and chemosensitive acute myeloid leukemia. Cytogenet Genome Res 2013; 141:272-6. [PMID: 23689423 DOI: 10.1159/000351219] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 03/04/2013] [Indexed: 11/19/2022] Open
Abstract
MicroRNA (miRNA) deregulation is associated with progression and treatment outcome in various types of cancers. To identify miRNAs related to therapeutic response, we applied an miRNA microarray followed by PCR verification of 33 available diagnostic bone marrow core biopsies from 33 acute myeloid leukemia patients including 15 chemoresistant and 18 chemosensitive patients. We found 3 significantly upregulated miRNAs, miR-363, miR-532-5p and miR-342-3p, related to therapeutic response (q < 0.05). Further validation of miR-532-5p and miR-363 expression by quantitative RT-PCR confirmed microarray analysis results. Genes targeted by miR-363 include RGS17 and HIPK3, both reported to be associated with drug response.
Collapse
Affiliation(s)
- N Mosakhani
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | | | | | | | | | | |
Collapse
|
47
|
Tuononen K, Mäki-Nevala S, Sarhadi VK, Wirtanen A, Rönty M, Salmenkivi K, Andrews JM, Telaranta-Keerie AI, Hannula S, Lagström S, Ellonen P, Knuuttila A, Knuutila S. Comparison of targeted next-generation sequencing (NGS) and real-time PCR in the detection of EGFR, KRAS, and BRAF mutations on formalin-fixed, paraffin-embedded tumor material of non-small cell lung carcinoma-superiority of NGS. Genes Chromosomes Cancer 2013; 52:503-11. [PMID: 23362162 DOI: 10.1002/gcc.22047] [Citation(s) in RCA: 130] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2012] [Accepted: 01/04/2013] [Indexed: 12/12/2022] Open
Abstract
The development of tyrosine kinase inhibitor treatments has made it important to test cancer patients for clinically significant gene mutations that influence the benefit of treatment. Targeted next-generation sequencing (NGS) provides a promising method for diagnostic purposes by enabling the simultaneous detection of multiple mutations in various genes in a single test. The aim of our study was to screen EGFR, KRAS, and BRAF mutations by targeted NGS and commonly used real-time polymerase chain reaction (PCR) methods to evaluate the feasibility of targeted NGS for the detection of the mutations. Furthermore, we aimed to identify potential novel mutations by targeted NGS. We analyzed formalin-fixed, paraffin-embedded (FFPE) tumor tissue specimens from 81 non-small cell lung carcinoma patients. We observed a significant concordance (from 96.3 to 100%) of the EGFR, KRAS, and BRAF mutation detection results between targeted NGS and real-time PCR. Moreover, targeted NGS revealed seven nonsynonymous single-nucleotide variations and one insertion-deletion variation in EGFR not detectable by the real-time PCR methods. The potential clinical significance of these variants requires elucidation in future studies. Our results support the use of targeted NGS in the screening of EGFR, KRAS, and BRAF mutations in FFPE tissue material.
Collapse
Affiliation(s)
- Katja Tuononen
- Department of Pathology, Haartman Institute, University of Helsinki, Helsinki, Finland
| | | | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
48
|
Guled M, Knuutila S. [MicroRNAs and cancer]. Duodecim 2013; 129:1661-1669. [PMID: 24069635] [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] [Subscribe] [Scholar Register] [Indexed: 06/02/2023]
Abstract
MicroRNAs (miRNAs) are group of noncoding RNAs that have been shown to regulate posttranscriptional gene expression. They have been under intense investigation since their association with cancer a decade ago. Genome wide detection methods have been developed to identify miRNA profiles in variety of biological systems and to confirm their involvement in different physiological and pathological processes. MiRNA implication in cancer pathology (tumor development, progression and response to therapy), perhaps the most widely studied miRNA topic, make them potential diagnostic, prognostic and predictive biomarkers. Currently, researchers are exploiting the possibilities of miRNA-based anti-cancer therapies and in the near future such therapies alone or in combination with other treatment modalities might be a reality.
Collapse
Affiliation(s)
- Mohamed Guled
- Helsingin yliopisto, Haartman-Instituutti, patologian osasto
| | | |
Collapse
|
49
|
Knuutila S. Biomarker analysis in human neoplasias: superior next-generation sequencing on frozen bone marrow cells and on formalin-fixed, paraffin-embedded tumor tissues. BMC Proc 2013; 7 Suppl 2:K18. [PMID: 24764475 PMCID: PMC3624673 DOI: 10.1186/1753-6561-7-s2-k18] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Affiliation(s)
- Sakari Knuutila
- Department of Pathology and Genetics, Haartman Institute, Helsinki University and HUSLAB, Finland
| |
Collapse
|
50
|
Mosakhani N, Pazzaglia L, Benassi MS, Borze I, Quattrini I, Picci P, Knuutila S. MicroRNA expression profiles in metastatic and non-metastatic giant cell tumor of bone. Histol Histopathol 2012; 28:671-8. [PMID: 23172052 DOI: 10.14670/hh-28.671] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Abstract
Giant cell tumor of bone (GCTB) is a skeletal neoplasm, a locally aggressive tumor that occasionally metastasizes to the lungs. To identify novel biomarkers associated with GCTB progression and metastasis, we performed a miRNA microarray on ten primary tumors of GCTB, of which five developed lung metastases and the rest remained metastasis-free. Between metastatic and non-metastatic GCTB, 12 miRNAs were differentially expressed (such as miR-136, miR-513a-5p, miR-494, miR-224, and miR-542-5p). A decreased level of miR-136 in metastatic versus non-metastatic GCTB was significantly confirmed by the quantitative reverse transcriptase polymerase chain reaction (qRT-PCR) (p=0.04). To identify potential target genes for the differentially expressed miRNAs, we used three target prediction databases. Then, to functionally validate the potential target genes of the differentially expressed miRNAs, we re-analyzed our previous gene expression data from the same ten patients. Eight genes such as NFIB, TNC, and FLRT2 were inversely expressed relative to their predicted miRNA regulators. NFIB expression correlated in metastatic GCTB with no or low expression of miR-136, and this gene was selected for further verification with qRT-PCR and immunohistochemistry. Verification of NFIB mRNA and protein by qRT-PCR showed elevated expression levels in metastatic GCTBs. Further, the protein expression level of NFIB was tested in an independent validation cohort of 74 primary archival GCTB specimens. In the primary tumors that developed metastases compared to the disease-free group, NFIB protein was moderately to strongly expressed at a higher frequency. Thus, in GCTB, miR-136 and NFIB may serve as prognostic makers.
Collapse
Affiliation(s)
- Neda Mosakhani
- Department of Pathology, Haartman Institute and HUSLAB, University of Helsinki and Helsinki University Central Hospital, Helsinki, Finland
| | | | | | | | | | | | | |
Collapse
|