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Nevone A, Lattarulo F, Russo M, Panno G, Milani P, Basset M, Avanzini MA, Merlini G, Palladini G, Nuvolone M. A Strategy for the Selection of RT-qPCR Reference Genes Based on Publicly Available Transcriptomic Datasets. Biomedicines 2023; 11:biomedicines11041079. [PMID: 37189697 DOI: 10.3390/biomedicines11041079] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Revised: 03/23/2023] [Accepted: 03/27/2023] [Indexed: 04/05/2023] Open
Abstract
In the next-generation sequencing era, RT-qPCR is still widely employed to quantify levels of nucleic acids of interest due to its popularity, versatility, and limited costs. The measurement of transcriptional levels through RT-qPCR critically depends on reference genes used for normalization. Here, we devised a strategy to select appropriate reference genes for a specific clinical/experimental setting based on publicly available transcriptomic datasets and a pipeline for RT-qPCR assay design and validation. As a proof-of-principle, we applied this strategy to identify and validate reference genes for transcriptional studies of bone-marrow plasma cells from patients with AL amyloidosis. We performed a systematic review of published literature to compile a list of 163 candidate reference genes for RT-qPCR experiments employing human samples. Next, we interrogated the Gene Expression Omnibus to assess expression levels of these genes in published transcriptomic studies on bone-marrow plasma cells from patients with different plasma cell dyscrasias and identified the most stably expressed genes as candidate normalizing genes. Experimental validation on bone-marrow plasma cells showed the superiority of candidate reference genes identified through this strategy over commonly employed “housekeeping” genes. The strategy presented here may apply to other clinical and experimental settings for which publicly available transcriptomic datasets are available.
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Affiliation(s)
- Alice Nevone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Francesca Lattarulo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Monica Russo
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giada Panno
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Paolo Milani
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Marco Basset
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Maria Antonietta Avanzini
- Pediatric Hematology Oncology, Cell Factory, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giampaolo Merlini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Giovanni Palladini
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
| | - Mario Nuvolone
- Department of Molecular Medicine, University of Pavia, 27100 Pavia, Italy
- Amyloidosis Research and Treatment Center, Fondazione IRCCS Policlinico San Matteo, 27100 Pavia, Italy
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Qu Y, Zhang S, Qu Y, Guo H, Wang S, Wang X, Huang T, Zhou H. Novel Gene Signature Reveals Prognostic Model in Acute Myeloid Leukemia. Front Genet 2020; 11:566024. [PMID: 33193652 PMCID: PMC7655922 DOI: 10.3389/fgene.2020.566024] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 10/08/2020] [Indexed: 01/23/2023] Open
Abstract
Background Acute myeloid leukemia (AML) is a clonal malignant disease with poor prognosis and a low overall survival rate. Although many studies on the treatment and detection of AML have been conducted, the molecular mechanism of AML development and progression has not been fully elucidated. The present study was designed to pursuit the molecular mechanism of AML using a comprehensive bioinformatics analysis, and build an applicable model to predict the survival probability of AML patients in clinical use. Methods To simplify the complicated regulatory networks, we performed the gene co-expression and PPI network based on WGCNA and STRING database using modularization design. Two machine learning methods, A least absolute shrinkage and selector operation (LASSO) algorithm and support vector machine-recursive feature elimination (SVM-RFE), were used to filter the common hub genes by five-fold cross-validation. The candidate hub genes were used to build the predictive model of AML by the cox-proportional hazards analysis, and validated in The Cancer Genome Atlas (TCGA) cohort and ohsu cohort, which were reliable in the experimental verification by qRT-PCR and western blotting in mRNA and protein levels. Results Three hub genes, FLT3, CD177 and TTPAL were used to build a clinically applicable model to predict the survival probability of AML patients and divided them into high and low groups. To compare the survival ability of the model with the classical clinical features, we generated the nomogram. The model displayed the most risk points contrast to other clinical characteristics, which was compatible with the data of cox multivariate regression. Conclusion This study reveal the novel molecular mechanism of AML, and construct a clinical model significantly related to AML patient prognosis. We showed the integrated roles of critical pathways, hub genes associated, which provide potential targets and new research ideas for the treatment and early detection of AML.
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Affiliation(s)
- Ying Qu
- Department of Hematology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, China
| | - Shuying Zhang
- Department of Hematology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, China
| | - Yanzhang Qu
- Department of Hematology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, China
| | - Heng Guo
- Department of Hematology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, China
| | - Suling Wang
- Department of Hematology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, China
| | - Xuemei Wang
- Department of Hematology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, China
| | - Tianjiao Huang
- Department of Hematology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, China
| | - Hong Zhou
- Department of Hematology, The Second Affiliated Hospital of Qiqihar Medical College, Qiqihar, China
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Wang LL, Jiang ZC, Zhang CY, Gao Y. Malignant glomus tumor of the ileum mimicking GIST with distant metastasis without BRAF V600E mutation. INTERNATIONAL JOURNAL OF CLINICAL AND EXPERIMENTAL PATHOLOGY 2018; 11:5117-5125. [PMID: 31949590 PMCID: PMC6962914] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 09/19/2018] [Indexed: 06/10/2023]
Abstract
Glomus tumors arising in the gastrointestinal tract are rare and generally benign mesenchymal neoplasms that account for approximately 1% of all gastrointestinal soft tissue tumors. We report a unique case of malignant glomus tumor arising in the ileum of an elderly Chinese woman with widespread metastasis. The patient underwent local tumor resection for a presumed gastrointestinal stromal tumor (GIST). However, brain metastasis developed 2 years later, followed by a lesion in colon 6 months later and a subcutaneous mass of abdominal wall 12 months later. Then, local resections of all metastatic tumors were performed. Histopathology and immunohistochemical findings supported the diagnosis of malignant glomus tumor. Microscopic examination revealed that the primary and metastatic tumor cells shared common features: oval to spindle-shaped, with sharply defined cell membranes, round uniform nuclei, atypical mitotic figures, and variable necrosis. Immunohistochemical staining revealed positive expression of vimentin, SMA, caldesmon, MLH1, MSH2, MSH6, PMS2, SDHB and P53. Even with distant metastasis, the patient has been followed up for 28 months after the third operation without any radiotherapy and chemotherapy. To the best of our knowledge, this is the first report of a malignant glomus tumor arising from the ileum that metastasizes to the brain and abdominal wall with relatively favorable prognosis.
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Affiliation(s)
- Ling-Ling Wang
- Department of Pathology, Capital Medical University Affiliated Beijing Shijitan HospitalBeijing, China
| | - Zhong-Cai Jiang
- Department of Pathology, Aviation General HospitalBeijing, China
| | - Cheng-Yan Zhang
- Department of Pathology, Capital Medical University Affiliated Beijing Shijitan HospitalBeijing, China
| | - Ying Gao
- Department of Pathology, Capital Medical University Affiliated Beijing Shijitan HospitalBeijing, China
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Gyvyte U, Juzenas S, Salteniene V, Kupcinskas J, Poskiene L, Kucinskas L, Jarmalaite S, Stuopelyte K, Steponaitiene R, Hemmrich-Stanisak G, Hübenthal M, Link A, Franke S, Franke A, Pangonyte D, Lesauskaite V, Kupcinskas L, Skieceviciene J. MiRNA profiling of gastrointestinal stromal tumors by next-generation sequencing. Oncotarget 2017; 8:37225-37238. [PMID: 28402935 PMCID: PMC5514905 DOI: 10.18632/oncotarget.16664] [Citation(s) in RCA: 30] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2016] [Accepted: 03/12/2017] [Indexed: 12/12/2022] Open
Abstract
Deregulation of miRNAs has been observed virtually in all major types of cancer, whereas the miRNA signature in GIST is not well characterized yet. In this study the first high-throughput miRNA profiling of 15 paired GIST and adjacent normal tissue samples was performed using small RNA-seq approach and differentially expressed miRNAs as well as isomiRNAs were defined. Highly significantly deregulated miRNAs were selected for validation by Taq-Man low-density array in replication group of 40 paired samples. Validated miRNAs were further subjected to enrichment analysis, which revealed significantly enriched KEGG pathways in the main GIST associated pathways. Further, we used an integrated analysis of miRNA-mRNA correlations for KIT and PDGFRA target genes and found a significant correlation between all of the enriched miRNAs and their target gene KIT. Results of the phenotype analysis showed miR-509-3p to be up-regulated in epithelioid and mixed cell types compared to spindle type, whereas miR-215-5p showed negative correlation with risk grade of GIST. These data reveal a detailed miRNA profile of GIST and highlight new candidates that may be important in the development of malignant disease.
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Affiliation(s)
- Ugne Gyvyte
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Simonas Juzenas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Violeta Salteniene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Juozas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Lina Poskiene
- Department of Pathological Anatomy, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Laimutis Kucinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Sonata Jarmalaite
- Division of Human Genome Research Centre, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- National Cancer Institute, Vilnius, Lithuania
| | - Kristina Stuopelyte
- Division of Human Genome Research Centre, Institute of Biosciences, Life Sciences Center, Vilnius University, Vilnius, Lithuania
- National Cancer Institute, Vilnius, Lithuania
| | - Ruta Steponaitiene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | | | - Matthias Hübenthal
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Alexander Link
- Department of Gastroenterology, Hepatology and Infectious Diseases, Otto-von-Guericke University Hospital Magdeburg, Magdeburg, Germany
| | - Sabine Franke
- Institute of Pathology, Otto-von-Guericke University, Magdeburg, Germany
| | - Andre Franke
- Institute of Clinical Molecular Biology, Christian-Albrechts-University Kiel, Kiel, Germany
| | - Dalia Pangonyte
- Department of Pathological Anatomy, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Vaiva Lesauskaite
- Institute of Cardiology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Limas Kupcinskas
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
- Department of Gastroenterology, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
| | - Jurgita Skieceviciene
- Institute for Digestive Research, Academy of Medicine, Lithuanian University of Health Sciences, Kaunas, Lithuania
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Huss S, Pasternack H, Ihle MA, Merkelbach-Bruse S, Heitkötter B, Hartmann W, Trautmann M, Gevensleben H, Büttner R, Schildhaus HU, Wardelmann E. Clinicopathological and molecular features of a large cohort of gastrointestinal stromal tumors (GISTs) and review of the literature: BRAF mutations in KIT/PDGFRA wild-type GISTs are rare events. Hum Pathol 2017; 62:206-214. [PMID: 28159677 DOI: 10.1016/j.humpath.2017.01.005] [Citation(s) in RCA: 38] [Impact Index Per Article: 5.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/05/2016] [Revised: 01/03/2017] [Accepted: 01/05/2017] [Indexed: 12/27/2022]
Abstract
In KIT/PDGFRA wild-type gastrointestinal stromal tumors (wt-GISTs), BRAF mutations are regarded as alternative pathogenic events driving tumorigenesis. In our study, we aimed at analyzing a large cohort (n=444) of GISTs for BRAF mutations using molecular and immunohistochemical methods. More than 3000 GIST samples from caucasian patients were available in our GIST and Sarcoma Registry NRW. Of these, we selected 172 wt-GISTs to evaluate the frequency of BRAF mutations. Furthermore, 272 GISTs with a representative KIT and PDGFRA mutational status were selected. BRAF mutational status was evaluated by high-resolution melting analysis, Sanger sequencing, and VE1 immunohistochemistry. A BRAF mutation (p.V600E) was found in 7 cases (3.9%) of the wt-GIST cohort. In 2 cases, multiple synchronous tumors harbored the same somatic BRAF mutation. VE1 immunohistochemical staining had a sensitivity of 81.8% and a specificity of 97.5% to detect BRAF p.V600E mutations. Analyzing our cases and the cases reported in the literature (n=37), the percentage of intermediate and high-risk BRAF-mutated wt-GISTs (17/31; 54.8%) was comparable to that recorded for large GIST cohorts irrespective of the mutational status. BRAF mutations are rare events in wt-GISTs, and VE1 immunohistochemistry appears to be a valuable pre-screening tool for the detection of BRAF p.V600E mutations. BRAF mutations in GISTs do not seem to have a prognostic value per se. However, as BRAF inhibition represents a therapeutic option to control disease, we suggest the assessment of the BRAF mutational status, especially in the setting of advanced GIST disease.
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Affiliation(s)
- Sebastian Huss
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
| | - Helen Pasternack
- Pathology of the University Medical Center Schleswig-Holstein, Campus Luebeck and the Research Center Borstel, Leibniz Center for Medicine and Biosciences, Ratzeburger Allee 160, 23538 Luebeck, Germany.
| | - Michaela Angelika Ihle
- Institute of Pathology, University Hospital Cologne, Kerpener Strasse 62, 50937 Cologne, Germany.
| | - Sabine Merkelbach-Bruse
- Institute of Pathology, University Hospital Cologne, Kerpener Strasse 62, 50937 Cologne, Germany.
| | - Birthe Heitkötter
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
| | - Wolfgang Hartmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
| | - Marcel Trautmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
| | - Heidrun Gevensleben
- Institute of Pathology, University Hospital Bonn, Sigmund-Freud-Strasse 25, 53127 Bonn, Germany.
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Kerpener Strasse 62, 50937 Cologne, Germany.
| | - Hans-Ulrich Schildhaus
- Institute of Pathology, University Hospital Göttingen, Robert-Koch-Straße 40, 37075 Göttingen, Germany.
| | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Albert-Schweitzer-Campus 1, 48156 Münster, Germany.
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Künstlinger H, Fassunke J, Schildhaus HU, Brors B, Heydt C, Ihle MA, Mechtersheimer G, Wardelmann E, Büttner R, Merkelbach-Bruse S. FGFR2 is overexpressed in myxoid liposarcoma and inhibition of FGFR signaling impairs tumor growth in vitro. Oncotarget 2016; 6:20215-30. [PMID: 26036639 PMCID: PMC4652999 DOI: 10.18632/oncotarget.4046] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/20/2014] [Accepted: 04/22/2015] [Indexed: 01/14/2023] Open
Abstract
Myxoid liposarcomas account for more than one third of liposarcomas and about 10% of all adult soft tissue sarcomas. The tumors are characterized by specific chromosomal translocations leading to the chimeric oncogenes FUS-DDIT3 or EWS1R-DDIT3. The encoded fusion proteins act as aberrant transcription factors. Therefore, we implemented comparative expression analyses using whole-genome microarrays in tumor and fat tissue samples. We aimed at identifying differentially expressed genes which may serve as diagnostic or prognostic biomarkers or as therapeutic targets. Microarray analyses revealed overexpression of FGFR2 and other members of the FGF/FGFR family. Overexpression of FGFR2 was validated by qPCR, immunohistochemistry and western blot analysis in primary tumor samples. Treatment of the myxoid liposarcoma cell lines MLS 402 and MLS 1765 with the FGFR inhibitors PD173074, TKI258 (dovitinib) and BGJ398 as well as specific siRNAs reduced cell proliferation, induced apoptosis and delayed cell migration. Combination of FGFR inhibitors with trabectedin further increased the effect. Our study demonstrates overexpression of FGFR2 and a functional role of FGFR signaling in myxoid liposarcoma. As FGFR inhibition showed effects on proliferation and cell migration and induced apoptosis in vitro, our data indicate the potential use of FGFR inhibitors as a targeted therapy for these tumors.
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Affiliation(s)
- Helen Künstlinger
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | - Jana Fassunke
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | - Benedikt Brors
- Computational Oncology, German Cancer Research Center (DKFZ), Heidelberg, Germany
| | - Carina Heydt
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
| | | | | | - Eva Wardelmann
- Gerhard-Domagk-Institute of Pathology, University Hospital Münster, Münster, Germany
| | - Reinhard Büttner
- Institute of Pathology, University Hospital Cologne, Cologne, Germany
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Tissue-specific selection of optimal reference genes for expression analysis of anti-cancer drug-related genes in tumor samples using quantitative real-time RT-PCR. Exp Mol Pathol 2014; 98:375-81. [PMID: 25445497 DOI: 10.1016/j.yexmp.2014.10.014] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2014] [Accepted: 10/31/2014] [Indexed: 12/22/2022]
Abstract
Gene transcription analysis in clinical tumor samples can help with diagnosis, prognosis, and treatment of cancers. We aimed to identify the optimal reference genes for reliable expression analysis in various tumor samples by quantitative real-time reverse transcription polymerase chain reaction (qRT-PCR). Using a one-step TaqMan-based qRT-PCR, 5 commonly used reference genes (ACTB, GAPDH, RPLPO, GUSB, and TFRC) and 10 anticancer drug-related genes (TYMS, RRM1, TUBB3, STMN1, TOP2A, EGFR, VEGFR2, HER2, ERCC1, and BRCA1) were analyzed in 327 tissue samples from lung, rectal, colon, gastric, esophageal, and breast tumors. According to the expression stability assessments obtained by using three programs (geNorm, NormFinder, and BestKeeper) and a comprehensive ranking method, the optimal reference genes for lung, gastric, esophageal, and breast tumors were RPLPO, GAPDH, ACTB, and ACTB, respectively. For rectal tumors, a combination of the 3 most stable genes (GUSB, ACTB, and RPLPO) was suitable for qRT-PCR, whereas for colon tumors, a combination of the 4 most stable genes (GAPDH, ACTB, GUSB, and RPLPO) was optimal for qRT-PCR. Based on the expression data of target genes normalized against selected reference genes, the principal component analysis revealed 4 expression patterns in 6 different tissues. One pattern was observed in gastric, rectal, and colon tumor tissues, which are gastrointestinal tumors. Expressions in the breast, lung, and esophageal tissues were separately represented as one pattern. Our results could facilitate the practice of personalized cancer medicine based on the gene expression profile of the patients.
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Huss S, Künstlinger H, Wardelmann E, Kleine MA, Binot E, Merkelbach-Bruse S, Rüdiger T, Mittler J, Hartmann W, Büttner R, Schildhaus HU. A subset of gastrointestinal stromal tumors previously regarded as wild-type tumors carries somatic activating mutations in KIT exon 8 (p.D419del). Mod Pathol 2013; 26:1004-12. [PMID: 23599150 PMCID: PMC3701292 DOI: 10.1038/modpathol.2013.47] [Citation(s) in RCA: 45] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2012] [Revised: 01/02/2013] [Accepted: 01/02/2013] [Indexed: 01/11/2023]
Abstract
About 10-15% of gastrointestinal stromal tumors (GISTs) carry wild-type sequences in all hot spots of KIT and platelet-derived growth factor receptor alpha (PDGFRA) (wt-GISTs). These tumors are currently defined by having no mutations in exons 9, 11, 13, and 17 of the KIT gene and exons 12, 14, and 18 of the PDGFRA gene. Until now, the analysis of further exons is not recommended. However, we have previously published a report on a KIT exon 8 germline mutation, which was associated with familial GIST and mastocytosis. We therefore investigated whether KIT exon 8 mutations might also occur in sporadic GIST. We screened a cohort of 145 wt-GISTs from a total of 1351 cases from our registry for somatic mutations in KIT exon 8. Two primary GISTs with an identical exon 8 mutation (p.D419del) were detected, representing 1.4% of all the cases analyzed. Based on all GISTs from our registry, the overall frequency of KIT exon 8 mutations was 0.15%. The first tumor originating in the small bowel of a 53-year-old male patient had mostly a biphasic spindled-epithelioid pattern with a high proliferative activity (14 mitoses/50 HPF) combined with a second low proliferative spindle cell pattern (4/50 HPF). The patient developed multiple peritoneal metastases 29 months later. The second case represented a jejunal GIST in a 67-year old woman who is relapse-free under adjuvant imatinib treatment. We conclude that about 1-2% of GISTs being classified as 'wild type' so far might, in fact, carry KIT mutations in exon 8. Moreover, this mutational subtype was shown to be activating and imatinib sensitive in vitro. We therefore propose that screening for KIT exon 8 mutations should become a routine in the diagnostic work-up of GIST and that patients with an exon 8 mutation and a significant risk for tumor progression should be treated with imatinib.
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Affiliation(s)
- Sebastian Huss
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Helen Künstlinger
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Eva Wardelmann
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Michaela A Kleine
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Elke Binot
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | | | - Thomas Rüdiger
- Städtisches Klinikum Karlsruhe, Institute of Pathology, Karlsruhe, Germany
| | - Jens Mittler
- Department of General and Abdominal Surgery, University Hospital Mainz, Mainz, Germany
| | - Wolfgang Hartmann
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Reinhard Büttner
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany
| | - Hans-Ulrich Schildhaus
- Institute of Pathology, University of Cologne, Medical Center, Cologne, Germany,Institute of Pathology, University of Cologne, Medical Center, Kerpener Strasse 62, Cologne D-50924, Germany.
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Masvidal L, Alvarez A, Ruano L, de Gracia J, Larriba S, Casals T. GUSB and ATP2B4 are suitable reference genes for CFTR gene expression data normalization in nasal epithelium cells. J Cyst Fibros 2012; 11:398-404. [PMID: 22525089 DOI: 10.1016/j.jcf.2012.03.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2011] [Revised: 02/14/2012] [Accepted: 03/21/2012] [Indexed: 11/17/2022]
Abstract
BACKGROUND CFTR expression studies contribute in understanding the relationship between CFTR transcripts and clinical outcomes. Normalization of qPCR data is an essential step to determine target gene expression. Consequently, appropriate reference genes must be selected for each gene/tissue. In this work, we have assessed the suitability of four potential reference genes for CFTR expression analysis in nasal epithelium. METHODS B2M, GUSB, HPRT1 and ATP2B4 expression was evaluated in nasal epithelium samples (CFTR-wt controls, n=21; CFTR-splicing group, n=18) by RT-qPCR. Calibration curves were built and different analyses (geNorm, NormFinder, Mann-Whitney) were performed to evaluate gene expression stability between samples as well as between groups. RESULTS AND CONCLUSIONS We have applied an accurate approach to select reference genes for CFTR expression analysis in nasal epithelium. From the four genes assessed, GUSB and ATP2B4 have been validated as a reliable gene combination for CFTR gene qPCR data normalization.
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Affiliation(s)
- Laia Masvidal
- Human Molecular Genetics Group, IDIBELL, 08908 Barcelona, Spain
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