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Liu Y, Edrisi M, Yan Z, A Ogilvie H, Nakhleh L. NestedBD: Bayesian inference of phylogenetic trees from single-cell copy number profiles under a birth-death model. Algorithms Mol Biol 2024; 19:18. [PMID: 38685065 PMCID: PMC11059640 DOI: 10.1186/s13015-024-00264-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/09/2023] [Accepted: 03/27/2024] [Indexed: 05/02/2024] Open
Abstract
Copy number aberrations (CNAs) are ubiquitous in many types of cancer. Inferring CNAs from cancer genomic data could help shed light on the initiation, progression, and potential treatment of cancer. While such data have traditionally been available via "bulk sequencing," the more recently introduced techniques for single-cell DNA sequencing (scDNAseq) provide the type of data that makes CNA inference possible at the single-cell resolution. We introduce a new birth-death evolutionary model of CNAs and a Bayesian method, NestedBD, for the inference of evolutionary trees (topologies and branch lengths with relative mutation rates) from single-cell data. We evaluated NestedBD's performance using simulated data sets, benchmarking its accuracy against traditional phylogenetic tools as well as state-of-the-art methods. The results show that NestedBD infers more accurate topologies and branch lengths, and that the birth-death model can improve the accuracy of copy number estimation. And when applied to biological data sets, NestedBD infers plausible evolutionary histories of two colorectal cancer samples. NestedBD is available at https://github.com/Androstane/NestedBD .
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Affiliation(s)
- Yushu Liu
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, USA.
| | - Mohammadamin Edrisi
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, USA
| | - Zhi Yan
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, USA
| | - Huw A Ogilvie
- Department of Genetics, University of Texas MD Anderson Cancer Center, TX, 77030, Houston, USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, 6100 Main St, Houston, 77005, TX, USA
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2
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Lyu X, Li T, Zhu D, Cheng Y, Chen Y, He X, Li Z, Li S, Wu W, Geng S, Zhang M, Yao C, Li J, Li Y, Chang Y, Li Y, Zhu Z, Mao M, Song Y. Whole-genome sequencing as an alternative to analyze copy number abnormalities in acute myeloid leukemia and myelodysplastic syndrome. Leuk Lymphoma 2022; 63:2301-2310. [PMID: 35695096 DOI: 10.1080/10428194.2022.2080821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
Abstract
Copy number aberrations (CNA) are the core determinants for diagnosis, risk stratification and prognosis in acute myeloid leukemia (AML) and myelodysplastic syndrome (MDS). In this study, a shallow whole-genome sequencing-based assay, LeukoPrint, was utilized to depict genomic CNA profiles from the bone marrow of 137 newly diagnosed AML/MDS patients. It demonstrated 98.1% concordance of CNA profiles with cytogenetics and/or fluorescence in situ hybridization (FISH). It is advantageous in detecting CNAs of short segments (1 Mb) and from samples with low leukemic cell content, more accurate for describing complex karyotypes and less confounded by subjective bias. LeukoPrint improved the overall diagnostic yield by redefining the risk categories for 16 patients by presenting new information. In summary, LeukoPrint provided an automated, convenient, and cost-effective approach to describe genomic CNA profiles. It brought greater diagnostic yield and risk stratification information by incorporating into the routine cytogenetics based on the CNA-related criteria of standard ELN/IPSS-R guidelines.
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Affiliation(s)
- Xiaodong Lyu
- Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Tao Li
- Department of Hematology, The First Affiliated Hospital of Zhengzhou University, Zhengzhou, China
| | - Dandan Zhu
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Yuexin Cheng
- Department of Hematology, Yancheng No. 1 People's Hospital, Yancheng, China.,Department of Hematology, The Yancheng Clinical College of Xuzhou Medical University, Yancheng, China
| | - Yan Chen
- Research & Development, SeekIn Inc., Shenzhen, China
| | - Xiangxiang He
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Zhenling Li
- Department of Hematology, China-Japan Friendship Hospital, Beijing, China
| | - Shiyong Li
- Research & Development, SeekIn Inc., Shenzhen, China
| | - Wei Wu
- Research & Development, SeekIn Inc., Shenzhen, China
| | | | - Mengna Zhang
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Chunxiao Yao
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Jingshuai Li
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Yangwei Li
- Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Yinyin Chang
- Clinical Laboratories, Shenyou Bio, Zhengzhou, China
| | - Yuchun Li
- Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
| | - Zunmin Zhu
- Department of Hematology, Henan Provincial People's Hospital, Zhengzhou, China
| | - Mao Mao
- Research & Development, SeekIn Inc., Shenzhen, China.,Yonsei Song-Dang Institute for Cancer Research, Yonsei University, Seoul, Korea
| | - Yongping Song
- Central Laboratory, The Affiliated Cancer Hospital of Zhengzhou University and Henan Cancer Hospital, Zhengzhou, China
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3
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Van Paemel R, Vandeputte C, Raman L, Van Thorre J, Willems L, Van Dorpe J, Van Der Linden M, De Wilde J, De Koker A, Menten B, Devalck C, Vicha A, Grega M, Schleiermacher G, Iddir Y, Chicard M, van Zogchel L, Stutterheim J, Lak NSM, Tytgat GAM, Laureys G, Speleman F, De Wilde B, Lammens T, De Preter K, Van Roy N. The feasibility of using liquid biopsies as a complementary assay for copy number aberration profiling in routinely collected paediatric cancer patient samples. Eur J Cancer 2021; 160:12-23. [PMID: 34794856 DOI: 10.1016/j.ejca.2021.09.022] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2021] [Revised: 07/27/2021] [Accepted: 09/11/2021] [Indexed: 12/15/2022]
Abstract
BACKGROUND Paediatric tumours are often characterised by the presence of recurrent DNA copy number alterations (CNAs). These DNA copy number profiles, obtained from a tissue biopsy, can aid in the correct prognostic classification and therapeutic stratification of several paediatric cancer entities (e.g. MYCN amplification in neuroblastoma) and are part of the routine diagnostic practice. Liquid biopsies (LQBs) offer a potentially safer alternative for such invasive tumour tissue biopsies and can provide deeper insight into tumour heterogeneity. PROCEDURE The robustness and reliability of LQB CNA analyses was evaluated. We performed retrospective CNA profiling using shallow whole-genome sequencing (sWGS) on paired plasma circulating cell-free DNA (cfDNA) and tissue DNA samples from routinely collected samples from paediatric patients (n = 128) representing different tumour entities, including osteosarcoma, Ewing sarcoma, rhabdomyosarcoma, Wilms tumour, brain tumours and neuroblastoma. RESULTS Overall, we observed a good concordance between CNAs in tissue DNA and cfDNA. The main cause of CNA discordance was found to be low cfDNA sample quality (i.e. the ratio of cfDNA (<700 bp) and high molecular weight DNA (>700 bp)). Furthermore, CNAs were observed that were present in cfDNA and not in tissue DNA, or vice-versa. In neuroblastoma samples, no false-positives or false-negatives were identified for the detection of the prognostic marker MYCN amplification. CONCLUSION In future prospective studies, CNA analysis on LQBs that are of sufficient quality can serve as a complementary assay for CNA analysis on tissue biopsies, as either cfDNA or tissue DNA can contain CNAs that cannot be identified in the other biomaterial.
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Affiliation(s)
- Ruben Van Paemel
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium; Research Foundation Flanders, Belgium
| | - Charlotte Vandeputte
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Lennart Raman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jolien Van Thorre
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium
| | - Leen Willems
- Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Jo Van Dorpe
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Malaïka Van Der Linden
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Jilke De Wilde
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pathology, Ghent University Hospital, Ghent, Belgium
| | - Andries De Koker
- Center for Medical Biotechnology, Flemish Institute Biotechnology (VIB), Ghent, Belgium; Research Foundation Flanders, Belgium
| | - Björn Menten
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | | | - Ales Vicha
- Department of Pediatric Hematology and Oncology, Charles University, Second Faculty of Medicine and University Hospital Motol, Prague, Czech Republic
| | - Marek Grega
- Department of Pathology and Molecular Medicine, 2nd Faculty of Medicine, Charles University and Motol University Hospital, Prague, Czech Republic
| | - Gudrun Schleiermacher
- Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
| | - Yasmine Iddir
- Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
| | - Mathieu Chicard
- Translational Pediatric Oncology, Centre de recherche de l'Institut Curie, Paris, France
| | - Lieke van Zogchel
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | | | - Nathalie S M Lak
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands; Department of Experimental Immunohematology, Sanquin Research and Landsteiner Laboratory, Amsterdam University Medical Center, Amsterdam, the Netherlands
| | - G A M Tytgat
- Princess Máxima Center for Pediatric Oncology, Utrecht, the Netherlands
| | - Geneviève Laureys
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Frank Speleman
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Bram De Wilde
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Tim Lammens
- Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Pediatric Hematology, Oncology and Stem Cell Transplantation, Ghent University Hospital, Ghent, Belgium
| | - Katleen De Preter
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium
| | - Nadine Van Roy
- Center for Medical Genetics, Ghent University Hospital, Ghent, Belgium; Cancer Research Institute Ghent (CRIG), Ghent, Belgium; Department of Biomolecular Medicine, Ghent University, Ghent, Belgium.
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4
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Roura AJ, Gielniewski B, Pilanc P, Szadkowska P, Maleszewska M, Krol SK, Czepko R, Kaspera W, Wojtas B, Kaminska B. Identification of the immune gene expression signature associated with recurrence of high-grade gliomas. J Mol Med (Berl) 2020; 99:241-255. [PMID: 33215304 DOI: 10.1007/s00109-020-02005-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 10/26/2020] [Accepted: 10/29/2020] [Indexed: 12/21/2022]
Abstract
High-grade gliomas (HGGs), the most common and aggressive primary brain tumors in adults, inevitably recur due to incomplete surgery or resistance to therapy. Intratumoral genomic and cellular heterogeneity of HGGs contributes to therapeutic resistance, recurrence, and poor clinical outcomes. Transcriptomic profiles of HGGs at recurrence have not been investigated in detail. Using targeted sequencing of cancer-related genes and transcriptomics, we identified single nucleotide variations, small insertions and deletions, copy number aberrations (CNAs), as well as gene expression changes and pathway deregulation in 16 pairs of primary and recurrent HGGs. Most of the somatic mutations identified in primary HGGs were not detected after relapse, suggesting a subclone substitution during the tumor progression. We found a novel frameshift insertion in the ZNF384 gene which may contribute to extracellular matrix remodeling. An inverse correlation of focal CNAs in EGFR and PTEN genes was detected. Transcriptomic analysis revealed downregulation of genes involved in messenger RNA splicing, cell cycle, and DNA repair, while genes related to interferon signaling and phosphatidylinositol (PI) metabolism are upregulated in secondary HGGs when compared to primary HGGs. In silico analysis of the tumor microenvironment identified M2 macrophages and immature dendritic cells as enriched in recurrent HGGs, suggesting a prominent immunosuppressive signature. Accumulation of those cells in recurrent HGGs was validated by immunostaining. Our findings point to a substantial transcriptomic deregulation and a pronounced infiltration of immature dendritic cells in recurrent HGG, which may impact the effectiveness of frontline immunotherapies in the GBM management. KEY MESSAGES: Most of the somatic mutations identified in primary HGGs were not detected after relapse. Focal CNAs in EGFR and PTEN genes are inversely correlated in primary and recurrent HGGs. Transcriptomic changes and distinct immune-related signatures characterize HGG recurrence. Recurrent HGGs are characterized by a prominent infiltration of immature dendritic and M2 macrophages.
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Affiliation(s)
| | | | - Paulina Pilanc
- Nencki Institute of Experimental Biology, Warsaw, Poland
| | | | | | - Sylwia K Krol
- Nencki Institute of Experimental Biology, Warsaw, Poland
| | - Ryszard Czepko
- Clinical Department of Neurosurgery, St. Raphael Hospital, Andrzej Frycz Modrzewski Krakow University, Krakow, Poland
| | - Wojciech Kaspera
- Department of Neurosurgery, Regional Hospital, Medical University of Silesia, Sosnowiec, Poland
| | - Bartosz Wojtas
- Nencki Institute of Experimental Biology, Warsaw, Poland.
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5
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Abstract
Copy number aberrations (CNAs), which are pathogenic copy number variations (CNVs), play an important role in the initiation and progression of cancer. Single-cell DNA-sequencing (scDNAseq) technologies produce data that is ideal for inferring CNAs. In this review, we review eight methods that have been developed for detecting CNAs in scDNAseq data, and categorize them according to the steps of a seven-step pipeline that they employ. Furthermore, we review models and methods for evolutionary analyses of CNAs from scDNAseq data and highlight advances and future research directions for computational methods for CNA detection from scDNAseq data.
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Affiliation(s)
- Xian F. Mallory
- Department of Computer Science, Rice University, Houston, TX USA
- Department of Computer Science, Florida State University, Tallahassee, FL USA
| | | | - Nicholas Navin
- Department of Genetics, the University of Texas M.D. Anderson Cancer Center, Houston, TX USA
| | - Luay Nakhleh
- Department of Computer Science, Rice University, Houston, TX USA
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6
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Hunter SM, Dall GV, Doyle MA, Lupat R, Li J, Allan P, Rowley SM, Bowtell D, Campbell IG, Gorringe KL. Molecular comparison of pure ovarian fibroma with serous benign ovarian tumours. BMC Res Notes 2020; 13:349. [PMID: 32698852 PMCID: PMC7376903 DOI: 10.1186/s13104-020-05194-z] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2020] [Accepted: 07/17/2020] [Indexed: 01/10/2023] Open
Abstract
OBJECTIVE Ovarian fibromas and adenofibromas are rare ovarian tumours. They are benign tumours composed of spindle-like stromal cells (pure fibroma) or a mixture of fibroblast and epithelial components (adenofibroma). We have previously shown that 40% of benign serous ovarian tumours are likely primary fibromas due to the neoplastic alterations being restricted to the stromal compartment of these tumours. We further explore this finding by comparing benign serous tumours to pure fibromas. RESULTS Performing copy number aberration (CNA) analysis on the stromal component of 45 benign serous tumours and 8 pure fibromas, we have again shown that trisomy of chromosome 12 is the most common aberration in ovarian fibromas. CNAs were more frequent in the pure fibromas than the benign serous tumours (88% vs 33%), however pure fibromas more frequently harboured more than one CNA event compared with benign serous tumours. As these extra CNA events observed in the pure fibromas were unique to this subset our data indicates a unique tumour evolution. Gene expression analysis on the two cohorts was unable to show gene expression changes that differed based on tumour subtype. Exome analysis did not reveal any recurrently mutated genes.
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Affiliation(s)
- Sally M Hunter
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Genevieve V Dall
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - Maria A Doyle
- Bioinformatics Core Facility Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Richard Lupat
- Bioinformatics Core Facility Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Jason Li
- Bioinformatics Core Facility Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Prue Allan
- Anatomical Pathology, Peter MacCallum Cancer Centre, East Melbourne, Victoria, Australia
| | - Simone M Rowley
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia
| | - David Bowtell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia.,The Department of Pathology, University of Melbourne, Parkville, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | | | - Ian G Campbell
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia.,The Department of Pathology, University of Melbourne, Parkville, Australia.,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia
| | - Kylie L Gorringe
- Cancer Genomics Program, Peter MacCallum Cancer Centre, East Melbourne, Australia. .,The Department of Pathology, University of Melbourne, Parkville, Australia. .,The Sir Peter MacCallum Department of Oncology, University of Melbourne, Parkville, Australia. .,Peter MacCallum Cancer Centre, Locked Bag 1, A'Beckett Street, Melbourne, VIC, 8006, Australia.
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7
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Bao H, Gao J, Chen YH, Altman JK, Frankfurt O, Wilson AL, Sukhanova M, Chen Q, Lu X. Rare myeloid sarcoma with KMT2A (MLL)-ELL fusion presenting as a vaginal wall mass. Diagn Pathol 2019; 14:26. [PMID: 30922345 PMCID: PMC6440110 DOI: 10.1186/s13000-019-0804-6] [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] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2018] [Accepted: 03/18/2019] [Indexed: 12/17/2022] Open
Abstract
Backgroud Myeloid sarcoma (MS) is a rare neoplasm of immature myeloid precursors that form tumor mass outside the bone marrow. The diagnosis of de novo MS can be challenging, particularly in patients with no prior history of hematologic malignancies or when MS involves unusual anatomic sites. Case presentation The patient was a 53-year-old woman with a history of uterine fibroids and vaginal bleeding for many years who presented with a vaginal wall mass. The tumor had histologic and phenotypic features of histiocytic sarcoma, however, overlapping with a possible extramedullary MS. Using a comprehensive genomic profiling, we were able to identify recurrent chromosomal aberrations associated with MS including a rare KMT2A-ELL fusion, losses of chromosomes 1p, 9, 10, 15, 18, and gain of chromosome 1q and mutations in FLT3 and PTPN11, and achived the final diagnosis of a de novo MS. The patient received standard treatment for acute myeloid leukemia regimen with stem cell transplantation and achieved complete remission. Conclusion Our case illustrates the clinical utility of comprehensive genomic profiling in assisting the diagnosis or differential diagnosis of challenging MS or histiocytic sarcoma cases, and in providing important information in tumor biology for appropriate clinical management.
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Affiliation(s)
- Haiyan Bao
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, ward 3-140, Chicago, IL, 60611, USA.,Department of Hematology, The first affiliated hospital of Soochow Univervisty, Suzhou, Jiangsu, China
| | - Juehua Gao
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, ward 3-140, Chicago, IL, 60611, USA
| | - Yi-Hua Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, ward 3-140, Chicago, IL, 60611, USA
| | - Jessica K Altman
- Department of Hematology-Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Olga Frankfurt
- Department of Hematology-Oncology, Northwestern University Feinberg School of Medicine, Chicago, IL, USA
| | - Amanda L Wilson
- Department of Pathology, Aurora Medical Center, Pathology, Kenosha, WI, USA
| | - Madina Sukhanova
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, ward 3-140, Chicago, IL, 60611, USA
| | - Qing Chen
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, ward 3-140, Chicago, IL, 60611, USA
| | - Xinyan Lu
- Department of Pathology, Northwestern University Feinberg School of Medicine, 303 East Chicago Avenue, ward 3-140, Chicago, IL, 60611, USA.
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8
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Carter MD, Durham AB, Miedema JR, Harms PW, Chan MP, Patel RM, Lowe L, Fullen DR, Hristov AC, Wang M, Andea AA. Molecular testing of borderline cutaneous melanocytic lesions: SNP array is more sensitive and specific than FISH. Hum Pathol 2018; 86:115-123. [PMID: 30576704 DOI: 10.1016/j.humpath.2018.12.002] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 07/27/2018] [Revised: 11/29/2018] [Accepted: 12/07/2018] [Indexed: 12/19/2022]
Abstract
Melanocytic lesions with borderline features are diagnostically challenging. Single-nucleotide polymorphism (SNP) arrays, which detect genomic copy number alterations (CNAs), can be helpful in distinguishing between nevi and melanoma. Fluorescence in situ hybridization (FISH) has been used as a more rapid, less expensive alternative to SNP array, using a panel of probes that are often gained or lost in melanoma. We used SNP array data from 63 borderline cutaneous melanocytic lesions and 44 definitive melanomas to predict the performance of FISH testing. Lesions were considered positive by "virtual FISH" if 1 or more of the 5 FISH-probed loci demonstrated appropriate CNAs by SNP array. Cases were classified as positive by SNP array if ≥3 CNAs were present, based on internal validation studies, or if FISH criteria were met. Conventional FISH was performed in 33 cases (17 borderline lesions, 16 melanomas). Of the 63 borderline cases, 44 (70%) were positive by SNP array and 30 (48%) were positive by virtual FISH. A higher proportion of melanomas were positive by SNP array (41/44, 93% sensitivity) and virtual FISH (36/44, 82% sensitivity). Virtual FISH had 61% sensitivity in the borderline group using SNP array as the gold standard, whereas specificity was 84%. There was good correlation between conventional and virtual FISH, with agreement in 30 of 33 (91%) cases. Although FISH is highly effective in distinguishing between nevi and melanoma in cases where the histological diagnosis is straightforward, it is not nearly as sensitive or specific as SNP array when applied to borderline lesions.
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Affiliation(s)
- Michael D Carter
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Alison B Durham
- Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Jayson R Miedema
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Paul W Harms
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602; Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - May P Chan
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602; Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Rajiv M Patel
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602; Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Lori Lowe
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602; Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Douglas R Fullen
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602; Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Alexandra C Hristov
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602; Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Min Wang
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
| | - Aleodor A Andea
- Department of Pathology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602; Department of Dermatology, Michigan Medicine, University of Michigan, Ann Arbor, MI, USA 48109-5602.
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9
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Kanagal-Shamanna R, Hodge JC, Tucker T, Shetty S, Yenamandra A, Dixon-McIver A, Bryke C, Huxley E, Lennon PA, Raca G, Xu X, Jeffries S, Quintero-Rivera F, Greipp PT, Slovak ML, Iqbal MA, Fang M. Assessing copy number aberrations and copy neutral loss of heterozygosity across the genome as best practice: An evidence based review of clinical utility from the cancer genomics consortium (CGC) working group for myelodysplastic syndrome, myelodysplastic/myeloproliferative and myeloproliferative neoplasms. Cancer Genet 2018; 228-229:197-217. [PMID: 30377088 DOI: 10.1016/j.cancergen.2018.07.003] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [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: 03/11/2018] [Revised: 07/27/2018] [Accepted: 07/30/2018] [Indexed: 12/16/2022]
Abstract
Multiple studies have demonstrated the utility of chromosomal microarray (CMA) testing to identify clinically significant copy number alterations (CNAs) and copy-neutral loss-of-heterozygosity (CN-LOH) in myeloid malignancies. However, guidelines for integrating CMA as a standard practice for diagnostic evaluation, assessment of prognosis and predicting treatment response are still lacking. CMA has not been recommended for clinical work-up of myeloid malignancies by the WHO 2016 or the NCCN 2017 guidelines but is a suggested test by the European LeukaemiaNet 2013 for the diagnosis of primary myelodysplastic syndrome (MDS). The Cancer Genomics Consortium (CGC) Working Group for Myeloid Neoplasms systematically reviewed peer-reviewed literature to determine the power of CMA in (1) improving diagnostic yield, (2) refining risk stratification, and (3) providing additional genomic information to guide therapy. In this manuscript, we summarize the evidence base for the clinical utility of array testing in the workup of MDS, myelodysplastic/myeloproliferative neoplasms (MDS/MPN) and myeloproliferative neoplasms (MPN). This review provides a list of recurrent CNAs and CN-LOH noted in this disease spectrum and describes the clinical significance of the aberrations and how they complement gene mutation findings by sequencing. Furthermore, for new or suspected diagnosis of MDS or MPN, we present suggestions for integrating genomic testing methods (CMA and mutation testing by next generation sequencing) into the current standard-of-care clinical laboratory testing (karyotype, FISH, morphology, and flow).
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Affiliation(s)
- Rashmi Kanagal-Shamanna
- Department of Hematopathology, The University of Texas M.D. Anderson Cancer Center, Houston TX, USA.
| | - Jennelle C Hodge
- Department of Medical and Molecular Genetics, Indiana University School of Medicine, Indianapolis, IN, USA; Department of Pediatrics, University of California Los Angeles, Los Angeles, CA, USA; Department of Pathology and Laboratory Medicine, Cedars-Sinai Medical Center, Los Angeles, CA, USA
| | - Tracy Tucker
- Department of Pathology and Laboratory Medicine, Cancer Genetics Laboratory, British Columbia Cancer Agency, Vancouver, BC Canada
| | - Shashi Shetty
- Department of Pathology, UHCMC, University Hospitals and Case Western Reserve University, Cleveland, OH, USA
| | - Ashwini Yenamandra
- Department of Pathology, Microbiology and Immunology, Vanderbilt University Medical Center, Nashville, TN, USA
| | | | - Christine Bryke
- Department of Pathology, Beth Israel Deaconess Medical Center, Harvard Medical School, Boston, MA, USA
| | - Emma Huxley
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | | | - Gordana Raca
- Department of Pathology and Laboratory Medicine, Children's Hospital of Los Angeles, Los Angeles, CA, USA
| | - Xinjie Xu
- ARUP Laboratories, University of Utah, Salt Lake City, UT, USA
| | - Sally Jeffries
- West Midlands Regional Genetics Laboratory, Birmingham Women's and Children's NHS Foundation Trust, Birmingham, UK
| | - Fabiola Quintero-Rivera
- Department of Pathology and Laboratory Medicine, UCLA Clinical Genomics Center, University of California Los Angeles, Los Angeles, CA, USA
| | - Patricia T Greipp
- Department of Laboratory Medicine and Pathology, Genomics Laboratory, Mayo Clinic, Rochester, MN, USA
| | - Marilyn L Slovak
- TriCore Reference Laboratories, University of New Mexico, Albuquerque, NM, USA
| | - M Anwar Iqbal
- University of Rochester Medical Center, Rochester, NY, USA
| | - Min Fang
- Fred Hutchinson Cancer Research Center and University of Washington, Seattle, WA, USA.
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10
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Carter MD, Gaston D, Huang WY, Greer WL, Pasternak S, Ly TY, Walsh NM. Genetic profiles of different subsets of Merkel cell carcinoma show links between combined and pure MCPyV-negative tumors. Hum Pathol 2017; 71:117-125. [PMID: 29079179 DOI: 10.1016/j.humpath.2017.10.014] [Citation(s) in RCA: 50] [Impact Index Per Article: 7.1] [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] [Received: 08/16/2017] [Revised: 10/06/2017] [Accepted: 10/13/2017] [Indexed: 01/31/2023]
Abstract
Tumorigenesis in Merkel cell carcinoma (MCC) is driven by (1) clonal integration of the Merkel cell polyomavirus (MCPyV) in neoplastic cells and/or (2) genetic damage by ultraviolet (UV) light. A higher mutational burden, a UV-mutational signature, and many mutations in the TP53 and RB1 genes characterize the virus-negative subset. MCPyV-negative MCCs include combined (often squamous and neuroendocrine) and pure (neuroendocrine) tumors. Because a combined morphology could elude detection microscopically, we sought a genetic link between combined and pure virus-negative tumors. From a global cohort of 46 cases, 9 pure MCPyV-positive, 9 pure MCPyV-negative, and 10 combined MCPyV-negative MCCs were studied by genome-wide microarray in search of copy number aberrations. The entire cohort (n=46) was evaluated by next-generation sequencing for mutations in selected tumor suppressor genes and oncogenes. More copy number aberrations and a greater fraction of the genome were changed in combined and pure MCPyV-negative tumors relative to MCPyV-positive cases (P<.01 for all comparisons). No difference in these parameters was found between the 2 MCPyV-negative groups. Copy number loss of RB1 or an inactivating RB1 mutation (either or both) was common in combined (8/10, 80%) and pure (7/9, 78%) MCPyV-negative tumors but not MCPyV-positive cases (1/9, 11%). A similar trend was seen for TP53 (combined [2/10, 20%] and pure virus-negative tumors [5/9, 56%] showed gene copy number loss or mutations contrasted with pure virus-positive cases [0/9, 0%]). The shared genetic profiles of combined and pure MCPyV-negative tumors link these subsets and separate them from MCPyV-positive tumors.
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Affiliation(s)
- Michael D Carter
- Department of Pathology and Laboratory Medicine (DPLM), Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, Nova Scotia, Canada B3H 1V8; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8.
| | - Dan Gaston
- Department of Pathology and Laboratory Medicine (DPLM), Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, Nova Scotia, Canada B3H 1V8; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8
| | - Weei-Yuarn Huang
- Department of Pathology and Laboratory Medicine (DPLM), Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, Nova Scotia, Canada B3H 1V8; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8
| | - Wenda L Greer
- Department of Pathology and Laboratory Medicine (DPLM), Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, Nova Scotia, Canada B3H 1V8; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8
| | - Sylvia Pasternak
- Department of Pathology and Laboratory Medicine (DPLM), Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, Nova Scotia, Canada B3H 1V8; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8
| | - Thai Yen Ly
- Department of Pathology and Laboratory Medicine (DPLM), Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, Nova Scotia, Canada B3H 1V8; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8
| | - Noreen M Walsh
- Department of Pathology and Laboratory Medicine (DPLM), Queen Elizabeth II Health Sciences Centre, Nova Scotia Health Authority (Central Zone), Halifax, Nova Scotia, Canada B3H 1V8; Department of Pathology, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8; Department of Medicine, Dalhousie University, Halifax, Nova Scotia, Canada B3H 1V8
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11
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Sinha N, Gaston D, Manders D, Goudie M, Matsuoka M, Xie T, Huang WY. Characterization of genome-wide copy number aberrations in colonic mixed adenoneuroendocrine carcinoma and neuroendocrine carcinoma reveals recurrent amplification of PTGER4 and MYC genes. Hum Pathol. 2018;73:16-25. [PMID: 28899736 DOI: 10.1016/j.humpath.2017.08.036] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 06/28/2017] [Revised: 08/29/2017] [Accepted: 08/30/2017] [Indexed: 12/15/2022]
Abstract
Colonic mixed adenoneuroendocrine carcinoma (MANEC) is an aggressive neoplasm with worse prognosis compared with adenocarcinoma. To gain a better understanding of the molecular features of colonic MANEC, we characterized the genome-wide copy number aberrations of 14 MANECs and 5 neuroendocrine carcinomas using the OncoScan FFPE (Affymetrix, Santa Clara, CA) assay. Compared with 269 colonic adenocarcinomas, 19 of 42 chromosomal arms of MANEC exhibited a similar frequency of major aberrant events as adenocarcinomas, and 13 chromosomal arms exhibited a higher frequency of copy number gains. Among them, the most significant chromosomal arms were 5p (77% versus 13%, P = .000012) and 8q (85% versus 33%, P = .0018). The Genomic Identification of Significant Targets in Cancers algorithm identified 7 peaks that drive the tumorgenesis of MANEC. For all except 5p13.1, the peaks largely overlapped with those of adenocarcinoma. Two tumors exhibited MYC amplification localized in 8q24.21, and 2 tumors exhibited PTGER4 amplification localized in 5p13.1. A total of 8 tumors exhibited high copy number gain of PTGER4 and/or MYC. Whereas the frequency of MYC amplification was similar to adenocarcinoma (10.5% versus 4%, P = .2), the frequency of PTGER4 amplification was higher than adenocarcinoma (10.5% versus 0.3%, P = .01). Our study demonstrates similar, but also distinct, copy number aberrations in MANEC compared with adenocarcinoma and suggests an important role for the MYC pathway of colonic carcinoma with neuroendocrine differentiation. The discovery of recurrent PTGER4 amplification implies a potential of exploring targeting therapy to the prostaglandin synthesis pathways in a subset of these tumors.
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12
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Berg KCG, Eide PW, Eilertsen IA, Johannessen B, Bruun J, Danielsen SA, Bjørnslett M, Meza-Zepeda LA, Eknæs M, Lind GE, Myklebost O, Skotheim RI, Sveen A, Lothe RA. Multi-omics of 34 colorectal cancer cell lines - a resource for biomedical studies. Mol Cancer 2017; 16:116. [PMID: 28683746 PMCID: PMC5498998 DOI: 10.1186/s12943-017-0691-y] [Citation(s) in RCA: 210] [Impact Index Per Article: 30.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/05/2017] [Accepted: 06/28/2017] [Indexed: 12/19/2022] Open
Abstract
Background Colorectal cancer (CRC) cell lines are widely used pre-clinical model systems. Comprehensive insights into their molecular characteristics may improve model selection for biomedical studies. Methods We have performed DNA, RNA and protein profiling of 34 cell lines, including (i) targeted deep sequencing (n = 612 genes) to detect single nucleotide variants and insertions/deletions; (ii) high resolution DNA copy number profiling; (iii) gene expression profiling at exon resolution; (iv) small RNA expression profiling by deep sequencing; and (v) protein expression analysis (n = 297 proteins) by reverse phase protein microarrays. Results The cell lines were stratified according to the key molecular subtypes of CRC and data were integrated at two or more levels by computational analyses. We confirm that the frequencies and patterns of DNA aberrations are associated with genomic instability phenotypes and that the cell lines recapitulate the genomic profiles of primary carcinomas. Intrinsic expression subgroups are distinct from genomic subtypes, but consistent at the gene-, microRNA- and protein-level and dominated by two distinct clusters; colon-like cell lines characterized by expression of gastro-intestinal differentiation markers and undifferentiated cell lines showing upregulation of epithelial-mesenchymal transition and TGFβ signatures. This sample split was concordant with the gene expression-based consensus molecular subtypes of primary tumors. Approximately ¼ of the genes had consistent regulation at the DNA copy number and gene expression level, while expression of gene-protein pairs in general was strongly correlated. Consistent high-level DNA copy number amplification and outlier gene- and protein- expression was found for several oncogenes in individual cell lines, including MYC and ERBB2. Conclusions This study expands the view of CRC cell lines as accurate molecular models of primary carcinomas, and we present integrated multi-level molecular data of 34 widely used cell lines in easily accessible formats, providing a resource for preclinical studies in CRC. Electronic supplementary material The online version of this article (doi:10.1186/s12943-017-0691-y) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Kaja C G Berg
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Peter W Eide
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ina A Eilertsen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Bjarne Johannessen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Jarle Bruun
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Stine A Danielsen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Merete Bjørnslett
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Leonardo A Meza-Zepeda
- Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.,Department of Core Facilities and Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway
| | - Mette Eknæs
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Guro E Lind
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway
| | - Ola Myklebost
- Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.,Department of Core Facilities and Department of Tumor Biology, Institute for Cancer Research, Oslo University Hospital, Oslo, Norway.,Department of Clinical Science, University of Bergen, Bergen, Norway
| | - Rolf I Skotheim
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Anita Sveen
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway.,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway.,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway
| | - Ragnhild A Lothe
- Department of Molecular Oncology, Institute for Cancer Research & K.G.Jebsen Colorectal Cancer Research Centre, Oslo University Hospital, P.O.Box 4953 Nydalen, -0424, Oslo, NO, Norway. .,Center for Cancer Biomedicine, Institute for Clinical Medicine, University of Oslo, Oslo, Norway. .,Norwegian Cancer Genomic Consortium, Oslo University Hospital, Oslo, Norway.
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13
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Koczkowska M, Lipska-Ziętkiewicz BS, Iliszko M, Ryś J, Miettinen M, Lasota J, Biernat W, Harazin-Lechowska A, Kruczak A, Limon J. Application of high-resolution genomic profiling in the differential diagnosis of liposarcoma. Mol Cytogenet 2017; 10:7. [PMID: 28331547 PMCID: PMC5356274 DOI: 10.1186/s13039-017-0309-5] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [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: 12/20/2016] [Accepted: 03/06/2017] [Indexed: 01/04/2023] Open
Abstract
Background Rarity and heterogeneity of liposarcomas (LPS) make their diagnosis difficult even for sarcoma-experts pathologists. The molecular mechanism underlying the development and progression of liposarcomas (LPS) remains only partially known. In order to identify and compare the genomic profiles, we analyzed array-based comparative genomic hybridization (array-CGH) profiles of 66 liposarcomas, including well-differentiated (WDLPS), dedifferentiated (DDLPS) and myxoid (MLPS) subtypes. Results Copy number aberrations (CNAs) were identified in 98% of WDLPS and DDLPS and in 95% of MLPS cases. The minimal common region of amplification at 12q14.1q21.1 was observed in 96% of WDLPS and DDLPS cases. Four regions of CNAs, including losses of chromosome 6, 11 and 13 and gains of chromosome 14 were classified as recurrent in DDLPS; at least one was identified in 74% of DDLPS tumors. The DDLPS-associated losses were much more common in tumors with increased genomic complexity. In MLPS, the most frequent CNAs were losses of chromosome 6 (40%) and gains of chromosome 1 (30%), with the minimal overlapping regions 6q14.1q22.31 and 1q25.1q32.2, respectively. Conclusions Our findings show that the application of array-CGH allows to delineate clearly the genomic profiles of WDLPS, DDLPS and MLPS that reflect biological differences between these tumors. Although CNAs varied widely, the subtypes of tumors have characteristic genomic profiles that could facilitate the differential diagnosis of LPS subtypes, especially between WDLPS and DDLPS. Electronic supplementary material The online version of this article (doi:10.1186/s13039-017-0309-5) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Magdalena Koczkowska
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211 Gdansk, Poland
| | | | - Mariola Iliszko
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211 Gdansk, Poland
| | - Janusz Ryś
- Department of Tumor Pathology, M. Sklodowska-Curie Memorial Institute of Oncology, 11 Garncarska Street, 31-115 Krakow, Poland
| | - Markku Miettinen
- Laboratory of Pathology, National Cancer Institute, Building 10, Room B1B47, 10 Center Drive, Bethesda, 20892 MD USA
| | - Jerzy Lasota
- Laboratory of Pathology, National Cancer Institute, Building 10, Room B1B47, 10 Center Drive, Bethesda, 20892 MD USA
| | - Wojciech Biernat
- Department of Pathology, Medical University of Gdansk, 17 Smoluchowskiego Street, 80-214 Gdansk, Poland
| | - Agnieszka Harazin-Lechowska
- Department of Tumor Pathology, M. Sklodowska-Curie Memorial Institute of Oncology, 11 Garncarska Street, 31-115 Krakow, Poland
| | - Anna Kruczak
- Department of Tumor Pathology, M. Sklodowska-Curie Memorial Institute of Oncology, 11 Garncarska Street, 31-115 Krakow, Poland
| | - Janusz Limon
- Department of Biology and Genetics, Medical University of Gdansk, 1 Debinki Street, 80-211 Gdansk, Poland
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14
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Olar A, Wani KM, Wilson CD, Zadeh G, DeMonte F, Jones DTW, Pfister SM, Sulman EP, Aldape KD. Global epigenetic profiling identifies methylation subgroups associated with recurrence-free survival in meningioma. Acta Neuropathol 2017; 133:431-444. [PMID: 28130639 PMCID: PMC5600514 DOI: 10.1007/s00401-017-1678-x] [Citation(s) in RCA: 112] [Impact Index Per Article: 16.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2016] [Revised: 01/16/2017] [Accepted: 01/17/2017] [Indexed: 12/14/2022]
Abstract
Meningioma is the most common primary brain tumor and carries a substantial risk of local recurrence. Methylation profiles of meningioma and their clinical implications are not well understood. We hypothesized that aggressive meningiomas have unique DNA methylation patterns that could be used to better stratify patient management. Samples (n = 140) were profiled using the Illumina HumanMethylation450BeadChip. Unsupervised modeling on a training set (n = 89) identified 2 molecular methylation subgroups of meningioma (MM) with significantly different recurrence-free survival (RFS) times between the groups: a prognostically unfavorable subgroup (MM-UNFAV) and a prognostically favorable subgroup (MM-FAV). This finding was validated in the remaining 51 samples and led to a baseline meningioma methylation classifier (bMMC) defined by 283 CpG loci (283-bMMC). To further optimize a recurrence predictor, probes subsumed within the baseline classifier were subject to additional modeling using a similar training/validation approach, leading to a 64-CpG loci meningioma methylation predictor (64-MMP). After adjustment for relevant clinical variables [WHO grade, mitotic index, Simpson grade, sex, location, and copy number aberrations (CNAs)] multivariable analyses for RFS showed that the baseline methylation classifier was not significant (p = 0.0793). The methylation predictor, however, was significantly associated with tumor recurrence (p < 0.0001). CNAs were extracted from the 450k intensity profiles. Tumor samples in the MM-UNFAV subgroup showed an overall higher proportion of CNAs compared to the MM-FAV subgroup tumors and the CNAs were complex in nature. CNAs in the MM-UNFAV subgroup included recurrent losses of 1p, 6q, 14q and 18q, and gain of 1q, all of which were previously identified as indicators of poor outcome. In conclusion, our analyses demonstrate robust DNA methylation signatures in meningioma that correlate with CNAs and stratify patients by recurrence risk.
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Affiliation(s)
- Adriana Olar
- Departments of Pathology and Laboratory Medicine and Neurosurgery, Medical University of South Carolina and Hollings Cancer Center, 171 Ashley Ave., MSC 908, Charleston, SC, 29425, USA.
| | - Khalida M Wani
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 W Holcombe Blvd., Houston, TX, 77030, USA
| | - Charmaine D Wilson
- Center for Nursing Research, The University of Texas School of Nursing, 6901 Bertner St., Houston, TX, 77030, USA
| | - Gelareh Zadeh
- Princess Margaret Cancer Centre, MacFeeters-Hamilton Brain Tumour Centre, College Street 101, Toronto, M5G 1L7, ON, Canada
| | - Franco DeMonte
- Department of Neurosurgery, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - David T W Jones
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Network (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
| | - Stefan M Pfister
- Division of Pediatric Neurooncology, German Cancer Research Center (DKFZ), German Cancer Network (DKTK), Im Neuenheimer Feld 280, 69120, Heidelberg, Germany
- Department of Pediatric Hematology and Oncology, Heidelberg University Hospital, Im Neuenheimer Feld 430, 69120, Heidelberg, Germany
| | - Erik P Sulman
- Department of Translational Molecular Pathology, The University of Texas MD Anderson Cancer Center, 2130 W Holcombe Blvd., Houston, TX, 77030, USA
- Departments of Radiation Oncology and Genomic Medicine, The University of Texas MD Anderson Cancer Center, 1515 Holcombe Blvd., Houston, TX, 77030, USA
| | - Kenneth D Aldape
- Princess Margaret Cancer Centre, MacFeeters-Hamilton Brain Tumour Centre, College Street 101, Toronto, M5G 1L7, ON, Canada
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15
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Murria Estal R, Palanca Suela S, de Juan Jiménez I, Alenda Gonzalez C, Egoavil Rojas C, García-Casado Z, López Guerrero JA, Juan Fita MJ, Sánchez Heras AB, Segura Huerta Á, Santaballa Bertrán A, Chirivella González I, Llop García M, Pérez Simó G, Barragán González E, Bolufer Gilabert P. Relationship of immunohistochemistry, copy number aberrations and epigenetic disorders with BRCAness pattern in hereditary and sporadic breast cancer. Fam Cancer 2016; 15:193-200. [PMID: 26723934 DOI: 10.1007/s10689-015-9864-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.4] [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] [Indexed: 01/17/2023]
Abstract
The study aims to identify the relevance of immunohistochemistry (IHC), copy number aberrations (CNA) and epigenetic disorders in BRCAness breast cancers (BCs). We studied 95 paraffin included BCs, of which 41 carried BRCA1/BRCA2 germline mutations and 54 were non hereditary (BRCAX/Sporadic). Samples were assessed for BRCA1ness and CNAs by Multiplex Ligation-dependent Probe Amplification (MLPA); promoter methylation (PM) was assessed by methylation-specific-MLPA and the expression of miR-4417, miR-423-3p, miR-590-5p and miR-187-3p by quantitative RT-PCR. IHC markers Ki67, ER, PR, HER2, CK5/6, EGFR and CK18 were detected with specific primary antibodies (DAKO, Denmark). BRCAness association with covariates was performed using multivariate binary logistic regression (stepwise backwards Wald option). BRCA1/2 mutational status (p = 0.027), large tumor size (p = 0.041) and advanced histological grade (p = 0.017) among clinic-pathological variables; ER (p < 0.001) among IHC markers; MYC (p < 0.001) among CNA; APC (p = 0.065), ATM (p = 0.014) and RASSF1 (p = 0.044) among PM; and miR-590-5p (p = 0.001), miR-4417 (p = 0.019) and miR-423 (p = 0.013) among microRNA expression, were the selected parameters significantly related with the BRCAness status. The logistic regression performed with all these parameters selected ER+ as linked with the lack of BRCAness (p = 0.001) and MYC CNA, APC PM and miR-590-5p expression with BRCAness (p = 0.014, 0.045 and 0.007, respectively). In conclusion, the parameters ER expression, APC PM, MYC CNA and miR-590-5p expression, allowed detection of most BRCAness BCs. The identification of BRCAness can help establish a personalized medicine addressed to predict the response to specific treatments.
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Affiliation(s)
- Rosa Murria Estal
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Sarai Palanca Suela
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Inmaculada de Juan Jiménez
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | | | | | | | | | | | | | | | | | | | - Marta Llop García
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Gema Pérez Simó
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Eva Barragán González
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain
| | - Pascual Bolufer Gilabert
- Laboratory of Molecular Biology, Service of Clinical Analysis, University Hospital La Fe, Torre A 4ª planta, Avenida de Fernando Abril Martorell, no 106, 46026, Valencia, Spain.
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16
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Cresswell GD, Apps JR, Chagtai T, Mifsud B, Bentley CC, Maschietto M, Popov SD, Weeks ME, Olsen ØE, Sebire NJ, Pritchard-Jones K, Luscombe NM, Williams RD, Mifsud W. Intra-Tumor Genetic Heterogeneity in Wilms Tumor: Clonal Evolution and Clinical Implications. EBioMedicine 2016; 9:120-129. [PMID: 27333041 PMCID: PMC4972528 DOI: 10.1016/j.ebiom.2016.05.029] [Citation(s) in RCA: 55] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2016] [Revised: 05/23/2016] [Accepted: 05/25/2016] [Indexed: 11/30/2022] Open
Abstract
The evolution of pediatric solid tumors is poorly understood. There is conflicting evidence of intra-tumor genetic homogeneity vs. heterogeneity (ITGH) in a small number of studies in pediatric solid tumors. A number of copy number aberrations (CNA) are proposed as prognostic biomarkers to stratify patients, for example 1q+ in Wilms tumor (WT); current clinical trials use only one sample per tumor to profile this genetic biomarker. We multisampled 20 WT cases and assessed genome-wide allele-specific CNA and loss of heterozygosity, and inferred tumor evolution, using Illumina CytoSNP12v2.1 arrays, a custom analysis pipeline, and the MEDICC algorithm. We found remarkable diversity of ITGH and evolutionary trajectories in WT. 1q+ is heterogeneous in the majority of tumors with this change, with variable evolutionary timing. We estimate that at least three samples per tumor are needed to detect >95% of cases with 1q+. In contrast, somatic 11p15 LOH is uniformly an early event in WT development. We find evidence of two separate tumor origins in unilateral disease with divergent histology, and in bilateral WT. We also show subclonal changes related to differential response to chemotherapy. Rational trial design to include biomarkers in risk stratification requires tumor multisampling and reliable delineation of ITGH and tumor evolution.
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Affiliation(s)
| | - John R Apps
- UCL Institute of Child Health, London, United Kingdom; Department of Paediatric Haematology and Oncology, Great Ormond Street Hospital, London, United Kingdom
| | | | | | - Christopher C Bentley
- The Francis Crick Institute, London, United Kingdom; UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, United Kingdom
| | | | - Sergey D Popov
- Divisions of Molecular Pathology and Cancer Therapeutics, Institute of Cancer Research, London, United Kingdom
| | - Mark E Weeks
- UCL Institute of Child Health, London, United Kingdom
| | - Øystein E Olsen
- Department of Radiology, Great Ormond Street Hospital, London, United Kingdom
| | - Neil J Sebire
- UCL Institute of Child Health, London, United Kingdom; Department of Histopathology, Great Ormond Street Hospital, London, United Kingdom
| | - Kathy Pritchard-Jones
- UCL Institute of Child Health, London, United Kingdom; Department of Paediatric Haematology and Oncology, Great Ormond Street Hospital, London, United Kingdom
| | - Nicholas M Luscombe
- The Francis Crick Institute, London, United Kingdom; UCL Genetics Institute, Department of Genetics, Evolution & Environment, University College London, United Kingdom; Okinawa Institute of Science & Technology, Okinawa, Japan
| | | | - William Mifsud
- UCL Institute of Child Health, London, United Kingdom; Department of Histopathology, Great Ormond Street Hospital, London, United Kingdom.
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17
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Ulz P, Auer M, Heitzer E. Detection of Circulating Tumor DNA in the Blood of Cancer Patients: An Important Tool in Cancer Chemoprevention. Methods Mol Biol 2016; 1379:45-68. [PMID: 26608289 DOI: 10.1007/978-1-4939-3191-0_5] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/05/2023]
Abstract
Liquid biopsies represent novel promising tools to determine the impact of clonal heterogeneity on clinical outcomes with the potential to identify novel therapeutic targets in cancer patients. We developed a low-coverage whole-genome sequencing approach in order to noninvasively establish copy number aberrations in plasma DNA from metastasized cancer patients. Using plasma-Seq we were able to monitor genetic evolution including the acquirement of novel copy number changes, such as focal amplifications and chromosomal polysomies. The big advantage of our approach is that it can be performed on a benchtop sequencer, speed, and cost-effectiveness. Therefore, plasma-Seq represents an easy, fast, and affordable tool to provide the urgently needed genetic follow-up data. Here we describe our method including plasma DNA extraction, library preparation, and bioinformatic analyses.
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18
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Cao Y, Liu Y, Yang X, Liu X, Han N, Zhang K, Lin D. Estimation of the Survival of Patients With Lung Squamous Cell Carcinoma Using Genomic Copy Number Aberrations. Clin Lung Cancer 2015; 17:68-74.e5. [PMID: 26427646 DOI: 10.1016/j.cllc.2015.08.005] [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] [Subscribe] [Scholar Register] [Received: 06/01/2015] [Revised: 08/04/2015] [Accepted: 08/11/2015] [Indexed: 01/25/2023]
Abstract
BACKGROUND Estimation of the survival of patients with lung squamous cell carcinoma (SCC) on the basis of histopathology is inadequate. The aim of this study was to identify genomic regions with potential value for estimating the prognosis of these patients. PATIENTS AND METHODS Depending on their survival time, 100 patients with primary lung SCC were separated into high- or low-risk prognostic groups, and their copy number aberrations (CNAs) were analyzed using array-comparative genomic hybridization (array-CGH). RESULTS We identified 123 CNA regions that were significantly associated with survival. Among these regions, some have been reported previously (eg, amplifications of 8p12, 3q27.1, and loss of 9p21.3 and 13q34) but others have never been reported. For example, gains of 3q27.1, 5p13.2, and 5p13.3 were found to be associated with a favorable prognosis, but patients harboring gains of 11q23.3, 11q13.1, and 14q32.3, and deletions of 3p21.3 and 9p21.3 tended to have poor survival. Among the 123 CNA regions, 41 were further selected to construct a survival estimation model that could effectively separate SCC patients into high- or low-risk groups with an accuracy of 92%, sensitivity of 90%, and specificity of 94%. The results of the array-CGH were further validated in an independent cohort of 45 formalin-fixed, paraffin-embedded specimens using real-time polymerase chain reaction. CONCLUSION A number of CNA regions were found to be associated with the survival of SCC patients, and we were able to construct a model to estimate prognosis on the basis of these regions. Assessment of these CNAs could potentially assist in clinical decision-making regarding adjuvant therapy after surgery.
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Affiliation(s)
- Yan Cao
- Department of Pathology, Plastic Surgery Hospital, Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Yu Liu
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Xin Yang
- Department of Pathology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China; Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, P.R. China
| | - XiangYang Liu
- Department of Thoracic Surgical Oncology, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Naijun Han
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Kaitai Zhang
- State Key Laboratory of Molecular Oncology, Department of Etiology and Carcinogenesis, Cancer Institute (Hospital), Peking Union Medical College and Chinese Academy of Medical Sciences, Beijing, P.R. China
| | - Dongmei Lin
- Key laboratory of Carcinogenesis and Translational Research (Ministry of Education), Department of Pathology, Peking University Cancer Hospital and Institute, Beijing, P.R. China.
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19
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Pećina-Šlaus N, Gotovac K, Kafka A, Tomas D, Borovečki F. Genetic changes observed in a case of adult pilocytic astrocytoma revealed by array CGH analysis. Mol Cytogenet 2014; 7:95. [PMID: 25606054 PMCID: PMC4300045 DOI: 10.1186/s13039-014-0095-2] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2014] [Accepted: 11/27/2014] [Indexed: 11/25/2022] Open
Abstract
BACKGROUND A palette of copy number changes in a case of adult pilocytic astrocytoma analyzed by Array Comparative Genomic Hybridization (aCGH) is presented. Pilocytic astrocytomas are specific gliomas that are benign and biologically distinct and the molecular mechanisms responsible for their development remain unexplained. The aCGH was performed using SurePrint G3 Human CGH microarrays 4 × 180 K (Agilent Technologies). To ascertain whether some of the aberrations were of constitutive nature, we also analyzed the blood sample from the same patient. RESULTS The result of aCGH analysis demonstrated differences in the tumor tissue when compared to normal control on the array and also to autologous DNA from patient's blood. The total number of aberrations found in our case was 41 including 37 deletions and 4 amplifications. Whole chromosomal gains and losses were not observed. Collectively, our results showed three deletions and one amplification at 1p, two deletions at 2q, two deletions at 4q, two deletion at 5q, two deletions at 7p and two deletions at 7q; there were also three deletions at 8q, one deletion at 9p, one deletion at 10p, three deletions and one amplification at 10q. Chromosome 11 showed two deletions at 11p, while there was one deletion at 12p and one at 12q. Four deletions at 14q; two deletions at 15q, one amplification at 17q and one deletion at 17q; one deletion at 18p, two deletions at 22q and finally one deletion at Xp and one deletion and one amplification at Xq. Among the signaling pathways, olfactory transduction, Fc gamma R-mediated phagocytosis and p53 signaling pathway showed significant enrichment ascertained by gene ontology (GO) analysis using the DAVID software. CONCLUSIONS Our aCGH analysis is bringing subtle genomic alterations thus broadening genetic spectrum of adult pilocytic astrocytoma in order to offer new molecular biomarkers that will help in diagnostics and therapeutic decision-making.
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Affiliation(s)
- Nives Pećina-Šlaus
- />Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Šalata 12, 10000 Zagreb, Croatia
- />Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Kristina Gotovac
- />Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, and University Hospital Center Zagreb, Šalata 2, 10 000 Zagreb, Croatia
| | - Anja Kafka
- />Laboratory of Neurooncology, Croatian Institute for Brain Research, School of Medicine University of Zagreb, Šalata 12, 10000 Zagreb, Croatia
- />Department of Biology, School of Medicine, University of Zagreb, Šalata 3, 10000 Zagreb, Croatia
| | - Davor Tomas
- />Department of Pathology, School of Medicine, University of Zagreb, Šalata 10, 10000 Zagreb, Croatia
- />Hospital Center “Sisters of Charity”, Vinogradska 29, 10000 Zagreb, Croatia
| | - Fran Borovečki
- />Department for Functional Genomics, Center for Translational and Clinical Research, University of Zagreb School of Medicine, and University Hospital Center Zagreb, Šalata 2, 10 000 Zagreb, Croatia
- />Department of Neurology, University Hospital Center Zagreb, Kišpatićeva 12, 10000 Zagreb, Croatia
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Barbieri CE, Bangma CH, Bjartell A, Catto JWF, Culig Z, Grönberg H, Luo J, Visakorpi T, Rubin MA. The mutational landscape of prostate cancer. Eur Urol 2013; 64:567-76. [PMID: 23759327 DOI: 10.1016/j.eururo.2013.05.029] [Citation(s) in RCA: 153] [Impact Index Per Article: 13.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2013] [Accepted: 05/09/2013] [Indexed: 11/18/2022]
Abstract
CONTEXT Prostate cancer (PCa) is a clinically heterogeneous disease with marked variability in patient outcomes. Molecular characterization has revealed striking mutational heterogeneity that may underlie the variable clinical course of the disease. OBJECTIVE In this review, we discuss the common genomic alterations that form the molecular basis of PCa, their functional significance, and the potential to translate this knowledge into patient care. EVIDENCE ACQUISITION We reviewed the relevant literature, with a particular focus on recent studies on somatic alterations in PCa. EVIDENCE SYNTHESIS Advances in sequencing technology have resulted in an explosion of data regarding the mutational events underlying the development and progression of PCa. Heterogeneity is the norm; few abnormalities in specific genes are highly recurrent, but alterations in certain signaling pathways do predominate. These alterations include those in pathways known to affect tumorigenesis in a wide spectrum of tissues, such as the phosphoinositide 3-kinase/phosphatase and tensin homolog/Akt pathway, cell cycle regulation, and chromatin regulation. Alterations more specific to PCa are also observed, particularly gene fusions of ETS transcription factors and alterations in androgen signaling. Mounting data suggest that PCa can be subdivided based on a molecular profile of genetic alterations. CONCLUSIONS Major advances have been made in cataloging the genomic alterations in PCa and understanding the molecular mechanisms underlying the disease. These findings raise the possibility that PCa could soon transition from being a poorly understood, heterogeneous disease with a variable clinical course to being a collection of homogenous subtypes identifiable by molecular criteria, associated with distinct risk profiles, and perhaps amenable to specific management strategies or targeted therapies.
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Affiliation(s)
- Christopher E Barbieri
- Department of Urology, Weill Medical College of Cornell University, New York, NY 10021, USA.
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