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Hilhorst R, van den Berg A, Boender P, van Wezel T, Kievits T, de Wijn R, Ruijtenbeek R, Corver WE, Morreau H. Differentiating Benign from Malignant Thyroid Tumors by Kinase Activity Profiling and Dabrafenib BRAF V600E Targeting. Cancers (Basel) 2023; 15:4477. [PMID: 37760447 PMCID: PMC10527361 DOI: 10.3390/cancers15184477] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2023] [Revised: 08/28/2023] [Accepted: 09/05/2023] [Indexed: 09/29/2023] Open
Abstract
Differentiated non-medullary thyroid cancer (NMTC) can be effectively treated by surgery followed by radioactive iodide therapy. However, a small subset of patients shows recurrence due to a loss of iodide transport, a phenotype frequently associated with BRAF V600E mutations. In theory, this should enable the use of existing targeted therapies specifically designed for BRAF V600E mutations. However, in practice, generic or specific drugs aimed at molecular targets identified by next generation sequencing (NGS) are not always beneficial. Detailed kinase profiling may provide additional information to help improve therapy success rates. In this study, we therefore investigated whether serine/threonine kinase (STK) activity profiling can accurately classify benign thyroid lesions and NMTC. We also determined whether dabrafenib (BRAF V600E-specific inhibitor), as well as sorafenib and regorafenib (RAF inhibitors), can differentiate BRAF V600E from non-BRAF V600E thyroid tumors. Using 21 benign and 34 malignant frozen thyroid tumor samples, we analyzed serine/threonine kinase activity using PamChip®peptide microarrays. An STK kinase activity classifier successfully differentiated malignant (26/34; 76%) from benign tumors (16/21; 76%). Of the kinases analyzed, PKC (theta) and PKD1 in particular, showed differential activity in benign and malignant tumors, while oncocytic neoplasia or Graves' disease contributed to erroneous classifications. Ex vivo BRAF V600E-specific dabrafenib kinase inhibition identified 6/92 analyzed peptides, capable of differentiating BRAF V600E-mutant from non-BRAF V600E papillary thyroid cancers (PTCs), an effect not seen with the generic inhibitors sorafenib and regorafenib. In conclusion, STK activity profiling differentiates benign from malignant thyroid tumors and generates unbiased hypotheses regarding differentially active kinases. This approach can serve as a model to select novel kinase inhibitors based on tissue analysis of recurrent thyroid and other cancers.
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Affiliation(s)
- Riet Hilhorst
- PamGene International BV, 5211 HH ‘s-Hertogenbosch, The Netherlands; (R.H.)
| | | | - Piet Boender
- PamGene International BV, 5211 HH ‘s-Hertogenbosch, The Netherlands; (R.H.)
| | - Tom van Wezel
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands (H.M.)
| | - Tim Kievits
- PamGene International BV, 5211 HH ‘s-Hertogenbosch, The Netherlands; (R.H.)
| | - Rik de Wijn
- PamGene International BV, 5211 HH ‘s-Hertogenbosch, The Netherlands; (R.H.)
| | - Rob Ruijtenbeek
- PamGene International BV, 5211 HH ‘s-Hertogenbosch, The Netherlands; (R.H.)
| | - Willem E. Corver
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands (H.M.)
| | - Hans Morreau
- Leiden University Medical Center, 2333 ZA Leiden, The Netherlands (H.M.)
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2
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Addie RD, Kostidis S, Corver WE, Oosting J, Aminzadeh-Gohari S, Feichtinger RG, Kofler B, Aydemirli MD, Giera M, Morreau H. Metabolic reprogramming related to whole-chromosome instability in models for Hürthle cell carcinoma. Sci Rep 2020; 10:9578. [PMID: 32533088 PMCID: PMC7293353 DOI: 10.1038/s41598-020-66599-1] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2019] [Accepted: 05/19/2020] [Indexed: 12/21/2022] Open
Abstract
Hürthle cell carcinoma (HCC) is a recurrent subtype of non-medullary thyroid cancer. HCC is characterized by profound whole-chromosome instability (w-CIN), resulting in a near-homozygous genome (NHG), a phenomenon recently attributed to reactive oxygen species (ROS) generated during mitosis by malfunctioning mitochondria. We studied shared metabolic traits during standard and glucose-depleted cell culture in thyroid cancer cell lines (TCCLs), with or without a NHG, using quantitative analysis of extra and intracellular metabolites and ROS production following inhibition of complex III with antimycin A. We found that the XTC.UC1 and FTC-236 cell lines (both NHG) are functionally impaired in complex I and produce significantly more superoxide radicals than SW579 and BHP 2–7 (non-NHG) after challenge with antimycin A. FTC-236 showed the lowest levels of glutathione and SOD2. XTC.UC1 and FTC-236 both exhibited reduced glycolytic activity and utilization of alternative sources to meet energy demands. Both cell lines also shared low levels of α-ketoglutarate and high levels of creatine, phosphocreatine, uridine diphosphate-N-acetylglucosamine, pyruvate and acetylcarnitine. Furthermore, the metabolism of XTC.UC1 was skewed towards the de novo synthesis of aspartate, an effect that persisted even in glucose-free media, pointing to reductive carboxylation. Our data suggests that metabolic reprogramming and a subtle balance between ROS generation and scavenging/conversion of intermediates may be involved in ROS-induced w-CIN in HCC and possibly also in rare cases of follicular thyroid cancer showing a NHG.
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Affiliation(s)
- Ruben D Addie
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands.,Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Sarantos Kostidis
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Willem E Corver
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands.
| | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Sepideh Aminzadeh-Gohari
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Müllner Hauptstraße 48, 5020, Salzburg, Austria
| | - René G Feichtinger
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Müllner Hauptstraße 48, 5020, Salzburg, Austria
| | - Barbara Kofler
- Research Program for Receptor Biochemistry and Tumor Metabolism, Department of Pediatrics, University Hospital of the Paracelsus Medical University, Müllner Hauptstraße 48, 5020, Salzburg, Austria
| | - Mehtap Derya Aydemirli
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Martin Giera
- Center for Proteomics and Metabolomics, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Albinusdreef 2, 2333ZA, Leiden, The Netherlands
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3
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Allelic Switching of DLX5, GRB10, and SVOPL during Colorectal Cancer Tumorigenesis. Int J Genomics 2019; 2019:1287671. [PMID: 31093489 PMCID: PMC6481143 DOI: 10.1155/2019/1287671] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/01/2018] [Revised: 01/28/2019] [Accepted: 02/07/2019] [Indexed: 11/26/2022] Open
Abstract
Allele-specific expression (ASE) is found in approximately 20-30% of human genes. During tumorigenesis, ASE changes due to somatic alterations that change the regulatory landscape. In colorectal cancer (CRC), many chromosomes show frequent gains or losses while homozygosity of chromosome 7 is rare. We hypothesized that genes essential to survival show allele-specific expression (ASE) on both alleles of chromosome 7. Using a panel of 21 recently established low-passage CRC cell lines, we performed ASE analysis by hybridizing DNA and cDNA to Infinium HumanExome-12 v1 BeadChips containing cSNPs in 392 chromosome 7 genes. The results of this initial analysis were extended and validated in a set of 89 paired normal mucosa and CRC samples. We found that 14% of genes showed ASE in one or more cell lines and identified allelic switching of the potential cell survival genes DLX5, GRB10, and SVOPL on chromosome 7, whereby the most abundantly expressed allele in the normal tissue is the lowest expressed allele in the tumor and vice versa. We established that this allelic switch does not result from loss of imprinting. The allelic switching of SVOPL may be a result of transcriptional downregulation, while the exact mechanisms resulting in the allelic switching of DLX5 and GRB10 remain to be elucidated. In conclusion, our results show that profound changes take place in allelic transcriptional regulation during the tumorigenesis of CRC.
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Corver WE, Demmers J, Oosting J, Sahraeian S, Boot A, Ruano D, Wezel TV, Morreau H. ROS-induced near-homozygous genomes in thyroid cancer. Endocr Relat Cancer 2018; 25:83-97. [PMID: 29066502 DOI: 10.1530/erc-17-0288] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 09/29/2017] [Accepted: 10/24/2017] [Indexed: 12/17/2022]
Abstract
A near-homozygous genome (NHG) is especially seen in a subset of follicular thyroid cancer of the oncocytic type (FTC-OV). An NHG was also observed in the metabolically relatively quiescent cell lines XTC.UC1, a model for FTC-OV, and in FTC-133, -236 and -238, the latter three derived from one single patient with follicular thyroid cancer. FTC-236 subclones showed subtle whole-chromosome differences indicative of sustained reciprocal mitotic missegregations. Reactive oxygen species (ROS) scavenger experiments reduced the number of chromosomal missegregations in XTC.UC1 and FTC-236, while pCHK2 was downregulated in these cells. Treatment with antimycin A increased ROS indicated by enhanced MitoSOX Red and pCHK2 fluorescence in metaphase cells. In a selected set of oncocytic follicular thyroid tumors, increasing numbers of whole-chromosome losses were observed toward an aggressive phenotype, but with retention of chromosome 7. Together, ROS activates CHK2 and links to the stepwise loss of whole chromosomes during tumor progression in these lesions. We postulate that sequential loss of whole chromosomes is a dominant driver of the oncogenesis of a subset of follicular thyroid tumors.
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Affiliation(s)
- Willem E Corver
- Department of Pathology Leiden University Medical CenterLeiden, Netherlands
| | - Joris Demmers
- Department of Pathology Leiden University Medical CenterLeiden, Netherlands
| | - Jan Oosting
- Department of Pathology Leiden University Medical CenterLeiden, Netherlands
| | - Shima Sahraeian
- Department of Pathology Leiden University Medical CenterLeiden, Netherlands
| | - Arnoud Boot
- Department of Pathology Leiden University Medical CenterLeiden, Netherlands
| | - Dina Ruano
- Department of Pathology Leiden University Medical CenterLeiden, Netherlands
| | - Tom van Wezel
- Department of Pathology Leiden University Medical CenterLeiden, Netherlands
| | - Hans Morreau
- Department of Pathology Leiden University Medical CenterLeiden, Netherlands
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5
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Hoekstra AS, Hensen EF, Jordanova ES, Korpershoek E, van der Horst-Schrivers AN, Cornelisse C, Corssmit EPM, Hes FJ, Jansen JC, Kunst HPM, Timmers HJLM, Bateman A, Eccles D, Bovée JVMG, Devilee P, Bayley JP. Loss of maternal chromosome 11 is a signature event in SDHAF2, SDHD, and VHL-related paragangliomas, but less significant in SDHB-related paragangliomas. Oncotarget 2017; 8:14525-14536. [PMID: 28099933 PMCID: PMC5362423 DOI: 10.18632/oncotarget.14649] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2016] [Accepted: 01/04/2017] [Indexed: 12/28/2022] Open
Abstract
Germline mutations in the succinate dehydrogenase (SDHA, SDHB, SDHC, SDHD, SDHAF2) or Von Hippel-Lindau (VHL) genes cause hereditary paraganglioma/pheochromocytoma. While SDHB (1p36) and VHL (3p25) are associated with autosomal dominant disease, SDHD (11q23) and SDHAF2 (11q13) show a remarkable parent-of-origin effect whereby tumor formation is almost completely dependent on paternal transmission of the mutant allele. Loss of the entire maternal copy of chromosome 11 occurs frequently in SDHD-linked tumors, and has been suggested to be the basis for this typical inheritance pattern.Using fluorescent in situ hybridization, microsatellite marker and SNP array analysis, we demonstrate that loss of the entire copy of chromosome 11 is also frequent in SDHAF2-related PGLs, occurring in 89% of tumors. Analysis of two imprinted differentially methylated regions (DMR) in 11p15, H19-DMR and KvDMR, showed that this loss always affected the maternal copy of chromosome 11. Likewise, loss of maternal chromosome 11p15 was demonstrated in 85% of SDHD and 75% of VHL-related PGLs/PCCs. By contrast, both copies of chromosome 11 were found to be retained in 62% of SDHB-mutated PGLs/PCCs, while only 31% showed loss of maternal chromosome 11p15. Genome-wide copy number analysis revealed frequent loss of 1p in SDHB mutant tumors and show greater genomic instability compared to SDHD and SDHAF2.These results show that loss of the entire copy of maternal chromosome 11 is a highly specific and statistically significant event in SDHAF2, SDHD and VHL-related PGLs/PCCs, but is less significant in SDHB-mutated tumors, suggesting that these tumors have a distinct genetic etiology.
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Affiliation(s)
- Attje S Hoekstra
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Erik F Hensen
- Department of Otolaryngology/Head and Neck Surgery, VU University Medical Center, Amsterdam, The Netherlands
| | | | - Esther Korpershoek
- Department of Pathology, Josephine Nefkens Institute, Erasmus Medical Center Rotterdam, Rotterdam, The Netherlands
| | | | - Cees Cornelisse
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Eleonora P M Corssmit
- Department of Endocrinology and Metabolic Diseases, Leiden University Medical Center, Leiden, The Netherlands
| | - Frederik J Hes
- Department of Clinical Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Jeroen C Jansen
- Department of Otorhinolaryngology, Leiden University Medical Center, Leiden, The Netherlands
| | - Henricus P M Kunst
- Department of Otorhinolaryngology, Head and Neck Surgery, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Henri J L M Timmers
- Department of Medicine, Division of Endocrinology, Radboud University Medical Centre, Nijmegen, The Netherlands
| | - Adrian Bateman
- Department of Cellular Pathology, University Hospital Southampton, Southampton, UK
| | - Diana Eccles
- University of Southampton School of Medicine, Cancer Sciences Division, Somers Cancer Research Building, Southampton, UK
| | - Judith V M G Bovée
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.,Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jean-Pierre Bayley
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
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6
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Bolognesi C, Forcato C, Buson G, Fontana F, Mangano C, Doffini A, Sero V, Lanzellotto R, Signorini G, Calanca A, Sergio M, Romano R, Gianni S, Medoro G, Giorgini G, Morreau H, Barberis M, Corver WE, Manaresi N. Digital Sorting of Pure Cell Populations Enables Unambiguous Genetic Analysis of Heterogeneous Formalin-Fixed Paraffin-Embedded Tumors by Next Generation Sequencing. Sci Rep 2016; 6:20944. [PMID: 26864208 PMCID: PMC4750064 DOI: 10.1038/srep20944] [Citation(s) in RCA: 33] [Impact Index Per Article: 4.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2015] [Accepted: 01/14/2016] [Indexed: 11/09/2022] Open
Abstract
Precision medicine in oncology requires an accurate characterization of a tumor molecular profile for patient stratification. Though targeted deep sequencing is an effective tool to detect the presence of somatic sequence variants, a significant number of patient specimens do not meet the requirements needed for routine clinical application. Analysis is hindered by contamination of normal cells and inherent tumor heterogeneity, compounded with challenges of dealing with minute amounts of tissue and DNA damages common in formalin-fixed paraffin-embedded (FFPE) specimens. Here we present an innovative workflow using DEPArray™ system, a microchip-based digital sorter to achieve 100%-pure, homogenous subpopulations of cells from FFPE samples. Cells are distinguished by fluorescently labeled antibodies and DNA content. The ability to address tumor heterogeneity enables unambiguous determination of true-positive sequence variants, loss-of-heterozygosity as well as copy number variants. The proposed strategy overcomes the inherent trade-offs made between sensitivity and specificity in detecting genetic variants from a mixed population, thus rescuing for analysis even the smaller clinical samples with low tumor cellularity.
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Affiliation(s)
| | | | | | | | | | | | | | | | | | | | | | | | | | | | | | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
| | | | - Willem E Corver
- Department of Pathology, Leiden University Medical Center, Leiden, Netherlands
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7
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Hoekstra AS, Devilee P, Bayley JP. Models of parent-of-origin tumorigenesis in hereditary paraganglioma. Semin Cell Dev Biol 2015; 43:117-124. [PMID: 26067997 DOI: 10.1016/j.semcdb.2015.05.011] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2015] [Revised: 05/27/2015] [Accepted: 05/28/2015] [Indexed: 02/07/2023]
Abstract
Paraganglioma and pheochromocytoma are neuroendocrine tumors that originate from either the sympathetic or the parasympathetic branches of the autonomic nervous system. Although 14 different genes have been linked to paraganglioma/pheochromocytoma, a subgroup of these genes is associated with hereditary paraganglioma-pheochromocytoma, the genes related to mitochondrial succinate dehydrogenase (SDH) including SDHA, SDHB, SDHC, SDHD and the assembly factor SDHAF2. Unlike mutations in other SDH subunit genes, mutations in SDHD and SDHAF2 show a remarkable parent-of-origin dependent tumorigenesis in which tumor formation almost exclusively occurs following paternal transmission of the mutation. To date, three different models have sought to explain the striking inheritance pattern seen in SDHD and SDHAF2-linked families. Despite the fact that the models suffer to varying degrees from a lack of experimental verification, all three models have made some attempt to incorporate current data and understanding of this phenomenon. In this review, we discuss our present understanding of this phenomenon and describe the three models that seek to explain the inheritance pattern in SDHD and SDHAF2-linked families.
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Affiliation(s)
- Attje S Hoekstra
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands
| | - Peter Devilee
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands; Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jean-Pierre Bayley
- Department of Human Genetics, Leiden University Medical Center, Leiden, The Netherlands.
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8
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Copy number alterations and allelic ratio in relation to recurrence of rectal cancer. BMC Genomics 2015; 16:438. [PMID: 26048403 PMCID: PMC4458034 DOI: 10.1186/s12864-015-1550-0] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2014] [Accepted: 04/17/2015] [Indexed: 12/16/2022] Open
Abstract
Background In rectal cancer, total mesorectal excision surgery combined with preoperative (chemo)radiotherapy reduces local recurrence rates but does not improve overall patient survival, a result that may be due to the harmful side effects and/or co-morbidity of preoperative treatment. New biomarkers are needed to facilitate identification of rectal cancer patients at high risk for local recurrent disease. This would allow for preoperative (chemo)radiotherapy to be restricted to high-risk patients, thereby reducing overtreatment and allowing personalized treatment protocols. We analyzed genome-wide DNA copy number (CN) and allelic alterations in 112 tumors from preoperatively untreated rectal cancer patients. Sixty-six patients with local and/or distant recurrent disease were compared to matched controls without recurrence. Results were validated in a second cohort of tumors from 95 matched rectal cancer patients. Additionally, we performed a meta-analysis that included 42 studies reporting on CN alterations in colorectal cancer and compared results to our own data. Results The genomic profiles in our study were comparable to other rectal cancer studies. Results of the meta-analysis supported the hypothesis that colon cancer and rectal cancer may be distinct disease entities. In our discovery patient study cohort, allelic retention of chromosome 7 was significantly associated with local recurrent disease. Data from the validation cohort were supportive, albeit not statistically significant, of this finding. Conclusions We showed that retention of heterozygosity on chromosome 7 may be associated with local recurrence in rectal cancer. Further research is warranted to elucidate the mechanisms and effect of retention of chromosome 7 on the development of local recurrent disease in rectal cancer. Electronic supplementary material The online version of this article (doi:10.1186/s12864-015-1550-0) contains supplementary material, which is available to authorized users.
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9
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Corver WE, van Wezel T, Molenaar K, Schrumpf M, van den Akker B, van Eijk R, Ruano Neto D, Oosting J, Morreau H. Near-haploidization significantly associates with oncocytic adrenocortical, thyroid, and parathyroid tumors but not with mitochondrial DNA mutations. Genes Chromosomes Cancer 2014; 53:833-44. [DOI: 10.1002/gcc.22194] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/12/2014] [Accepted: 05/28/2014] [Indexed: 01/06/2023] Open
Affiliation(s)
- Willem E. Corver
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Tom van Wezel
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Kees Molenaar
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Melanie Schrumpf
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Brendy van den Akker
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Ronald van Eijk
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Dina Ruano Neto
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Jan Oosting
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
| | - Hans Morreau
- Department of Pathology; Leiden University Medical Center; RC Leiden Netherlands
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Glioblastomas are composed of genetically divergent clones with distinct tumourigenic potential and variable stem cell-associated phenotypes. Acta Neuropathol 2014; 127:203-19. [PMID: 24154962 PMCID: PMC3895194 DOI: 10.1007/s00401-013-1196-4] [Citation(s) in RCA: 80] [Impact Index Per Article: 8.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2013] [Revised: 10/10/2013] [Accepted: 10/13/2013] [Indexed: 12/23/2022]
Abstract
Glioblastoma (GBM) is known to be a heterogeneous disease; however, the genetic composition of the cells within a given tumour is only poorly explored. In the advent of personalised medicine the understanding of intra-tumoural heterogeneity at the cellular and the genetic level is mandatory to improve treatment and clinical outcome. By combining ploidy-based flow sorting with array-comparative genomic hybridization we show that primary GBMs present as either mono- or polygenomic tumours (64 versus 36 %, respectively). Monogenomic tumours were limited to a pseudodiploid tumour clone admixed with normal stromal cells, whereas polygenomic tumours contained multiple tumour clones, yet always including a pseudodiploid population. Interestingly, pseudodiploid and aneuploid fractions carried the same aberrations as defined by identical chromosomal breakpoints, suggesting that evolution towards aneuploidy is a late event in GBM development. Interestingly, while clonal heterogeneity could be recapitulated in spheroid-based xenografts, we find that genetically distinct clones displayed different tumourigenic potential. Moreover, we show that putative cancer stem cell markers including CD133, CD15, A2B5 and CD44 were present on genetically distinct tumour cell populations. These data reveal the clonal heterogeneity of GBMs at the level of DNA content, tumourigenic potential and stem cell marker expression, which is likely to impact glioma progression and treatment response. The combined knowledge of intra-tumour heterogeneity at the genetic, cellular and functional level is crucial to assess treatment responses and to design personalized treatment strategies for primary GBM.
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11
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The homeobox gene MEIS1 is methylated in BRAF (p.V600E) mutated colon tumors. PLoS One 2013; 8:e79898. [PMID: 24244575 PMCID: PMC3820613 DOI: 10.1371/journal.pone.0079898] [Citation(s) in RCA: 10] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Accepted: 09/26/2013] [Indexed: 12/18/2022] Open
Abstract
Development of colorectal cancer (CRC) can occur both via gene mutations in tumor suppressor genes and oncogenes, as well as via epigenetic changes, including DNA methylation. Site-specific methylation in CRC regulates expression of tumor-associated genes. Right-sided colon tumors more frequently have BRAF (p.V600E) mutations and have higher methylation grades when compared to left-sided malignancies. The aim of this study was to identify DNA methylation changes associated with BRAF (p.V600E) mutation status. We performed methylation profiling of colon tumor DNA, isolated from frozen sections enriched for epithelial cells by macro-dissection, and from paired healthy tissue. Single gene analyses comparing BRAF (p.V600E) with BRAF wild type revealed MEIS1 as the most significant differentially methylated gene (log2 fold change: 0.89, false discovery rate-adjusted P-value 2.8*10(-9)). This finding was validated by methylation-specific PCR that was concordant with the microarray data. Additionally, validation in an independent cohort (n=228) showed a significant association between BRAF (p.V600E) and MEIS1 methylation (OR: 13.0, 95% CI: 5.2 - 33.0, P<0.0001). MEIS1 methylation was associated with decreased MEIS1 gene expression in both patient samples and CRC cell lines. The same was true for gene expression of a truncated form of MEIS1, MEIS1 D27 , which misses exon 8 and has a proposed tumor suppression function. To trace the origin of MEIS1 promoter methylation, 14 colorectal tumors were flow-sorted. Four out of eight BRAF (p.V600E) tumor epithelial fractions (50%) showed MEIS1 promoter methylation, as well as three out of eight BRAF (p.V600E) stromal fractions (38%). Only one out of six BRAF wild type showed MEIS1 promoter methylation in both the epithelial tumor and stromal fractions (17%). In conclusion, BRAF (p.V600E) colon tumors showed significant MEIS1 promoter methylation, which was associated with decreased MEIS1 gene expression.
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12
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Adey A, Burton JN, Kitzman JO, Hiatt JB, Lewis AP, Martin BK, Qiu R, Lee C, Shendure J. The haplotype-resolved genome and epigenome of the aneuploid HeLa cancer cell line. Nature 2013; 500:207-11. [PMID: 23925245 PMCID: PMC3740412 DOI: 10.1038/nature12064] [Citation(s) in RCA: 252] [Impact Index Per Article: 22.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2012] [Accepted: 03/11/2013] [Indexed: 12/18/2022]
Abstract
The HeLa cell line was established in 1951 from cervical cancer cells taken from a patient, Henrietta Lacks, marking the first successful attempt to continually culture human-derived cells in vitro1. HeLa’s robust growth and unrestricted distribution resulted in its broad adoption – both intentionally and through widespread cross-contamination2 – and for the past sixty years it has served a role analogous to that of a model organism3. Its cumulative impact is illustrated by the fact that HeLa is named in >74,000 or ~0.3% of PubMed abstracts. The genomic architecture of HeLa remains largely unexplored beyond its karyotype4, in part because like many cancers, its extensive aneuploidy renders such analyses challenging. We performed haplotype-resolved whole genome sequencing5 of the HeLa CCL-2 strain, discovering point and indel variation, mapping copy-number and loss of heterozygosity (LOH), and phasing variants across full chromosome arms. We further investigated variation and copy-number profiles for HeLa S3 and eight additional strains. Surprisingly, HeLa is relatively stable with respect to point variation, accumulating few new mutations since early passaging. Haplotype resolution facilitated reconstruction of an amplified, highly rearranged region at chromosome 8q24.21 at which the HPV-18 viral genome integrated as the likely initial event underlying tumorigenesis. We combined these maps with RNA-Seq6 and ENCODE Project7 datasets to phase the HeLa epigenome, revealing strong, haplotype-specific activation of the proto-oncogene MYC by the integrated HPV-18 genome ~500 kilobases upstream, and permitting global analyses of the relationship between gene dosage and expression. These data provide an extensively phased, high-quality reference genome for past and future experiments relying on HeLa, and demonstrate the value of haplotype resolution for characterizing cancer genomes and epigenomes.
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Affiliation(s)
- Andrew Adey
- Department of Genome Sciences, University of Washington, Seattle, Washington 98115, USA
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van den Tillaart SAHM, Corver WE, Ruano Neto D, ter Haar NT, Goeman JJ, Trimbos JBMZ, Fleuren GJ, Oosting J. Loss of heterozygosity and copy number alterations in flow-sorted bulky cervical cancer. PLoS One 2013; 8:e67414. [PMID: 23874418 PMCID: PMC3706587 DOI: 10.1371/journal.pone.0067414] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2012] [Accepted: 05/20/2013] [Indexed: 01/05/2023] Open
Abstract
Treatment choices for cervical cancer are primarily based on clinical FIGO stage and the post-operative evaluation of prognostic parameters including tumor diameter, parametrial and lymph node involvement, vaso-invasion, infiltration depth, and histological type. The aim of this study was to evaluate genomic changes in bulky cervical tumors and their relation to clinical parameters, using single nucleotide polymorphism (SNP)-analysis. Flow-sorted tumor cells and patient-matched normal cells were extracted from 81 bulky cervical tumors. DNA-index (DI) measurement and whole genome SNP-analysis were performed. Data were analyzed to detect copy number alterations (CNA) and allelic balance state: balanced, imbalanced or pure LOH, and their relation to clinical parameters. The DI varied from 0.92–2.56. Pure LOH was found in ≥40% of samples on chromosome-arms 3p, 4p, 6p, 6q, and 11q, CN gains in >20% on 1q, 3q, 5p, 8q, and 20q, and losses on 2q, 3p, 4p, 11q, and 13q. Over 40% showed gain on 3q. The only significant differences were found between histological types (squamous, adeno and adenosquamous) in the lesser allele intensity ratio (LAIR) (p = 0.035) and in the CNA analysis (p = 0.011). More losses were found on chromosome-arm 2q (FDR = 0.004) in squamous tumors and more gains on 7p, 7q, and 9p in adenosquamous tumors (FDR = 0.006, FDR = 0.004, and FDR = 0.029). Whole genome analysis of bulky cervical cancer shows widespread changes in allelic balance and CN. The overall genetic changes and CNA on specific chromosome-arms differed between histological types. No relation was found with the clinical parameters that currently dictate treatment choice.
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Sarasqueta AF, Forte G, Corver WE, de Miranda NF, Ruano D, van Eijk R, Oosting J, Tollenaar RAEM, van Wezel T, Morreau H. Integral analysis of p53 and its value as prognostic factor in sporadic colon cancer. BMC Cancer 2013; 13:277. [PMID: 23739040 PMCID: PMC3682902 DOI: 10.1186/1471-2407-13-277] [Citation(s) in RCA: 34] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2012] [Accepted: 05/08/2013] [Indexed: 02/08/2023] Open
Abstract
BACKGROUND p53 (encoded by TP53) is involved in DNA damage repair, cell cycle regulation, apoptosis, aging and cellular senescence. TP53 is mutated in around 50% of human cancers. Nevertheless, the consequences of p53 inactivation in colon cancer outcome remain unclear. Recently, a new role of p53 together with CSNK1A1 in colon cancer invasiveness has been described in mice. METHODS By combining data on different levels of p53 inactivation, we aimed to predict p53 functionality and to determine its effects on colon cancer outcome. Moreover, survival effects of CSNK1A1 together with p53 were also studied.Eighty-three formalin fixed paraffin embedded colon tumors were enriched for tumor cells using flow sorting, the extracted DNA was used in a custom SNP array to determine chr17p13-11 allelic state; p53 immunostaining, TP53 exons 5, 6, 7 and 8 mutations were determined in combination with mRNA expression analysis on frozen tissue. RESULTS Patients with a predicted functional p53 had a better prognosis than patients with non functional p53 (Log Rank p=0.009). Expression of CSNK1A1 modified p53 survival effects. Patients with low CSNK1A1 expression and non-functional p53 had a very poor survival both in the univariate (Log Rank p<0.001) and in the multivariate survival analysis (HR=4.74 95% CI 1.45 - 15.3 p=0.009). CONCLUSION The combination of mutational, genomic, protein and downstream transcriptional activity data predicted p53 functionality which is shown to have a prognostic effect on colon cancer patients. This effect was specifically modified by CSKN1A1 expression.
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Barteneva NS, Ketman K, Fasler-Kan E, Potashnikova D, Vorobjev IA. Cell sorting in cancer research--diminishing degree of cell heterogeneity. Biochim Biophys Acta Rev Cancer 2013; 1836:105-22. [PMID: 23481260 DOI: 10.1016/j.bbcan.2013.02.004] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2013] [Revised: 02/06/2013] [Accepted: 02/08/2013] [Indexed: 12/18/2022]
Abstract
Increasing evidence of intratumor heterogeneity and its augmentation due to selective pressure of microenvironment and recent achievements in cancer therapeutics lead to the need to investigate and track the tumor subclonal structure. Cell sorting of heterogeneous subpopulations of tumor and tumor-associated cells has been a long established strategy in cancer research. Advancement in lasers, computer technology and optics has led to a new generation of flow cytometers and cell sorters capable of high-speed processing of single cell suspensions. Over the last several years cell sorting was used in combination with molecular biological methods, imaging and proteomics to characterize primary and metastatic cancer cell populations, minimal residual disease and single tumor cells. It was the principal method for identification and characterization of cancer stem cells. Analysis of single cancer cells may improve early detection of tumors, monitoring of circulating tumor cells, evaluation of intratumor heterogeneity and chemotherapeutic treatments. The aim of this review is to provide an overview of major cell sorting applications and approaches with new prospective developments such as microfluidics and microchip technologies.
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Affiliation(s)
- Natasha S Barteneva
- Program in Cellular and Molecular Medicine, Children's Hospital Boston, Harvard Medical School, Boston, MA, USA.
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Bravatà V, Cammarata FP, Forte GI, Minafra L. "Omics" of HER2-positive breast cancer. OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY 2013; 17:119-29. [PMID: 23421906 DOI: 10.1089/omi.2012.0099] [Citation(s) in RCA: 21] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
HER2/neu amplification/overexpression is the only somatic mutation widely considered to be a marker of disease outcome and response to treatment in breast cancer. Pathologists have made large efforts to achieve accuracy in characterizing HER2/neu status. The introduction of transtuzumab contributed to development of additional measures to identify sensitive and resistant subclasses of HER2/neu-positive tumors. In this article, we describe the latest advances in HER2/neu status diagnostic assessment and the most relevant research emerging from "Omics" (genomics, epigenetics, transcriptomics, and proteomics) studies on HER2/neu-positive breast cancer. A large quantity of biomarkers from different studies highlighted HER2/neu-positive specific proliferation, cell cycle arrest, and apoptosis mechanisms, as well as immunological and metabolic behavior. Major driver genes of tumor progression have had a candidate status (GRB7, MYC, CCND1, EGFR, etc.), even though the main role for HER2/neu is largely recognized. Nonetheless, existing omics data and HER2/neu-positive molecular profiles seem to suggest that few proteogenomic alterations in HER2, EGFR, and PI3K networks could significantly affect the effectiveness of transtuzumab. The systematic search of molecular alterations in and across these pathways can help to select the most appropriate drug for a given patient based on in-depth understanding of complexity in tumor biology.
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Affiliation(s)
- Valentina Bravatà
- Institute of Molecular Bioimaging and Physiology (IBFM), National Research Council (CNR), Cefalù Unit, Cefalù, Italy
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Holley T, Lenkiewicz E, Evers L, Tembe W, Ruiz C, Gsponer JR, Rentsch CA, Bubendorf L, Stapleton M, Amorese D, Legendre C, Cunliffe HE, McCullough AE, Pockaj B, Craig D, Carpten J, Von Hoff D, Iacobuzio-Donahue C, Barrett MT. Deep clonal profiling of formalin fixed paraffin embedded clinical samples. PLoS One 2012; 7:e50586. [PMID: 23226320 PMCID: PMC3511535 DOI: 10.1371/journal.pone.0050586] [Citation(s) in RCA: 41] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/16/2012] [Accepted: 10/23/2012] [Indexed: 01/15/2023] Open
Abstract
Formalin fixed paraffin embedded (FFPE) tissues are a vast resource of annotated clinical samples. As such, they represent highly desirable and informative materials for the application of high definition genomics for improved patient management and to advance the development of personalized therapeutics. However, a limitation of FFPE tissues is the variable quality of DNA extracted for analyses. Furthermore, admixtures of non-tumor and polyclonal neoplastic cell populations limit the number of biopsies that can be studied and make it difficult to define cancer genomes in patient samples. To exploit these valuable tissues we applied flow cytometry-based methods to isolate pure populations of tumor cell nuclei from FFPE tissues and developed a methodology compatible with oligonucleotide array CGH and whole exome sequencing analyses. These were used to profile a variety of tumors (breast, brain, bladder, ovarian and pancreas) including the genomes and exomes of matching fresh frozen and FFPE pancreatic adenocarcinoma samples.
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Affiliation(s)
- Tara Holley
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
| | - Elizabeth Lenkiewicz
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
| | - Lisa Evers
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
| | - Waibhav Tembe
- Collaborative Bioinformatics Center, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Christian Ruiz
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Joel R. Gsponer
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Cyrill A. Rentsch
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
- Department of Urology, University Hospital Basel, University of Basel, Basel, Switzerland
| | - Lukas Bubendorf
- Institute for Pathology, University Hospital Basel, University of Basel, Basel, Switzerland
| | | | - Doug Amorese
- NuGEN, San Carlos, California, United States of America
| | - Christophe Legendre
- Collaborative Bioinformatics Center, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Heather E. Cunliffe
- Computational Biology Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Ann E. McCullough
- Department of Laboratory Medicine, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - Barbara Pockaj
- Department of Surgery, Mayo Clinic, Scottsdale, Arizona, United States of America
| | - David Craig
- Neurogenomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - John Carpten
- Integrated Cancer Genomics Division, Translational Genomics Research Institute, Phoenix, Arizona, United States of America
| | - Daniel Von Hoff
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
- Virginia G. Piper Cancer Center, Scottsdale Healthcare, Scottsdale, Arizona, United States of America
| | | | - Michael T. Barrett
- Clinical Translational Research Division, Translational Genomics Research Institute, Scottsdale, Arizona, United States of America
- * E-mail:
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Corver WE, Ruano D, Weijers K, den Hartog WCE, van Nieuwenhuizen MP, de Miranda N, van Eijk R, Middeldorp A, Jordanova ES, Oosting J, Kapiteijn E, Hovens G, Smit J, van Wezel T, Morreau H. Genome haploidisation with chromosome 7 retention in oncocytic follicular thyroid carcinoma. PLoS One 2012; 7:e38287. [PMID: 22675538 PMCID: PMC3365880 DOI: 10.1371/journal.pone.0038287] [Citation(s) in RCA: 57] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/02/2011] [Accepted: 05/03/2012] [Indexed: 12/20/2022] Open
Abstract
Background Recurrent non-medullary thyroid carcinoma (NMTC) is a rare disease. We initially characterized 27 recurrent NMTC: 13 papillary thyroid cancers (PTC), 10 oncocytic follicular carcinomas (FTC-OV), and 4 non-oncocytic follicular carcinomas (FTC). A validation cohort composed of benign and malignant (both recurrent and non-recurrent) thyroid tumours was subsequently analysed (n = 20). Methods Data from genome-wide SNP arrays and flow cytometry were combined to determine the chromosomal dosage (allelic state) in these tumours, including mutation analysis of components of PIK3CA/AKT and MAPK pathways. Results All FTC-OVs showed a very distinct pattern of genomic alterations. Ten out of 10 FTC-OV cases showed near-haploidisation with or without subsequent genome endoreduplication. Near-haploidisation was seen in 5/10 as extensive chromosome-wide monosomy (allelic state [A]) with near-haploid DNA indices and retention of especially chromosome 7 (seen as a heterozygous allelic state [AB]). In the remaining 5/10 chromosomal allelic states AA with near diploid DNA indices were seen with allelic state AABB of chromosome 7, suggesting endoreduplication after preceding haploidisation. The latter was supported by the presence of both near-haploid and endoreduplicated tumour fractions in some of the cases. Results were confirmed using FISH analysis. Relatively to FTC-OV limited numbers of genomic alterations were identified in other types of recurrent NMTC studied, except for chromosome 22q which showed alterations in 6 of 13 PTCs. Only two HRAS, but no mutations of EGFR or BRAF were found in FTC-OV. The validation cohort showed two additional tumours with the distinct pattern of genomic alterations (both with oncocytic features and recurrent). Conclusions We demonstrate that recurrent FTC-OV is frequently characterised by genome-wide DNA haploidisation, heterozygous retention of chromosome 7, and endoreduplication of a near-haploid genome. Whether normal gene dosage on especially chromosome 7 (containing EGFR, BRAF, cMET) is crucial for FTC-OV tumour survival is an important topic for future research. Microarrays Data are made available at GEO (GSE31828).
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MESH Headings
- Adenocarcinoma, Follicular
- Aged
- Aged, 80 and over
- Alleles
- Carcinoma, Neuroendocrine
- Chromosomes, Human, Pair 7/genetics
- Cohort Studies
- DNA Mutational Analysis
- DNA, Neoplasm/genetics
- Disease Progression
- Female
- Flow Cytometry
- Gene Dosage/genetics
- Genes, Neoplasm/genetics
- Genome, Human/genetics
- Haploidy
- Homozygote
- Humans
- Male
- Middle Aged
- Models, Biological
- Oxyphil Cells/pathology
- Phenotype
- Polymorphism, Single Nucleotide/genetics
- Recurrence
- Reproducibility of Results
- Thyroid Neoplasms/genetics
- Thyroid Neoplasms/pathology
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Affiliation(s)
- Willem E. Corver
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail: (WEC); (HM)
| | - Dina Ruano
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Karin Weijers
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | | | - Noel de Miranda
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Anneke Middeldorp
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | | | - Jan Oosting
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Ellen Kapiteijn
- Department of Clinical Oncology, Leiden University Medical Center, Leiden, The Netherlands
| | - Guido Hovens
- Department of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Jan Smit
- Department of Endocrinology, Leiden University Medical Center, Leiden, The Netherlands
| | - Tom van Wezel
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
| | - Hans Morreau
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
- * E-mail: (WEC); (HM)
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19
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van Wezel T, Middeldorp A, Wijnen JT, Morreau H. A review of the genetic background and tumour profiling in familial colorectal cancer. Mutagenesis 2012; 27:239-45. [PMID: 22294773 DOI: 10.1093/mutage/ger071] [Citation(s) in RCA: 8] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/17/2022] Open
Abstract
Inherited predisposition plays a role in 10-30% of colorectal cancer (CRC) cases. Of the large families with a clearly positive family history of CRC, ∼40% is not affected by known CRC syndromes. The existence of families with unexplained forms of inherited CRC--familial CRC--suggests the presence of still unknown high- or moderate-risk CRC predisposing factors. While the genomic profiles of sporadic CRCs have been studied extensively, few studies have analysed the tumour profiles of hereditary or familial CRC. Here, we review recent advances in genomic tumour profiling in familial CRC in comparison with sporadic CRC. In addition, we discuss the role of known CRC risk factors in familial CRC.
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Affiliation(s)
- Tom van Wezel
- Department of Pathology, LUMC, Albinusdreef 2, 2333 ZA Leiden, The Netherlands.
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20
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Corver WE, Ter Haar NT, Fleuren GJ, Oosting J. Cervical carcinoma-associated fibroblasts are DNA diploid and do not show evidence for somatic genetic alterations. Cell Oncol (Dordr) 2011; 34:553-63. [PMID: 22042555 PMCID: PMC3223353 DOI: 10.1007/s13402-011-0061-5] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 09/05/2011] [Indexed: 02/03/2023] Open
Abstract
Background Cancer-associated fibroblasts (CAFs) have been recognized as important contributors to cancer development and progression. However, opposing evidence has been published whether CAFs, in addition to epigenetic, also undergo somatic genetic alterations and whether these changes contribute to carcinogenesis and tumour progression. Methods We combined multiparameter DNA flow cytometry, flow-sorting and 6K SNP-arrays to study DNA aneuploidy, % S-phase, loss of heterozygosity (LOH) and copy number alterations (CNAs) in cervical cancer-associated stromal cell fractions (n = 57) from formalin-fixed, paraffin-embedded (FFPE) samples. Tissue sections were examined for the presence of CAFs. Microsatellite analysis was used to confirm LOH findings. Results Smooth muscle actin and vimentin immunohistochemistry verified the presence of CAFs in all cases tested. However, we found no evidence for DNA aneuploidy, somatic genetic alterations in the vimentin-positive stromal cell fractions of any samples, while high frequencies of DNA content abnormalities (43/57) and substantial numbers of CNAs and LOH were identified in the keratin-positive epithelial cell fractions. LOH hot-spots on chromosomes 3p, 4p and 6p found were confirmed by microsatellite analysis. Conclusion From our study we conclude that stromal cell fractions from cervical carcinomas are DNA diploid, have a genotype undistinguishable from patient-matched normal tissue and are genetically stable. Using flow cytometry and SNP-arrays, stromal genetic changes do not seem to play a role during cervical carcinogenesis and progression. In addition, the stromal cell fraction of cervical carcinomas can be used as reference allowing large retrospective studies of archival FFPE tissues for which no normal reference tissue is available. Electronic supplementary material The online version of this article (doi:10.1007/s13402-011-0061-5) contains supplementary material, which is available to authorized users.
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Corver WE, ter Haar NT. High-resolution multiparameter DNA flow cytometry for the detection and sorting of tumor and stromal subpopulations from paraffin-embedded tissues. ACTA ACUST UNITED AC 2011; Chapter 7:7.37.1-7.37.21. [PMID: 21207360 DOI: 10.1002/0471142956.cy0737s55] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit contains a detailed protocol for the simultaneous flow cytometric measurement of tumor cells, stromal cells, and DNA content of formalin-fixed, paraffin-embedded (FFPE) tissues. The vimentin-positive stromal cell fraction can be used as an internal reference for DNA content assessments. This allows clear detection of keratin-positive tumor cells with a DNA index lower than 1.0 and of keratin-positive tumor cells with a DNA close to 1.0 in overall DNA aneuploid samples, thus improved DNA ploidy assessment in FFPE carcinomas. Furthermore, the protocol is useful for studying molecular genetic alterations and intratumor heterogeneity in archival FFPE samples. Keratin-positive tumor cell fractions can be flow-sorted for further molecular genetic analysis, while DNA from the sorted vimentin-positive stromal cells can serve as a reference when normal tissue of the patient is not available.
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22
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Pansuriya TC, Oosting J, Krenács T, Taminiau AHM, Verdegaal SHM, Sangiorgi L, Sciot R, Hogendoorn PCW, Szuhai K, Bovée JVMG. Genome-wide analysis of Ollier disease: Is it all in the genes? Orphanet J Rare Dis 2011; 6:2. [PMID: 21235737 PMCID: PMC3027091 DOI: 10.1186/1750-1172-6-2] [Citation(s) in RCA: 30] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2010] [Accepted: 01/14/2011] [Indexed: 01/06/2023] Open
Abstract
Background Ollier disease is a rare, non-hereditary disorder which is characterized by the presence of multiple enchondromas (ECs), benign cartilaginous neoplasms arising within the medulla of the bone, with an asymmetric distribution. The risk of malignant transformation towards central chondrosarcoma (CS) is increased up to 35%. The aetiology of Ollier disease is unknown. Methods We undertook genome-wide copy number and loss of heterozygosity (LOH) analysis using Affymetrix SNP 6.0 array on 37 tumours of 28 Ollier patients in combination with expression array using Illumina BeadArray v3.0 for 7 ECs of 6 patients. Results Non-recurrent EC specific copy number alterations were found at FAM86D, PRKG1 and ANKS1B. LOH with copy number loss of chromosome 6 was found in two ECs from two unrelated Ollier patients. One of these patients also had LOH at chromosome 3. However, no common genomic alterations were found for all ECs. Using an integration approach of SNP and expression array we identified loss as well as down regulation of POU5F1 and gain as well as up regulation of NIPBL. None of these candidate regions were affected in more than two Ollier patients suggesting these changes to be random secondary events in EC development. An increased number of genetic alterations and LOH were found in Ollier CS which mainly involves chromosomes 9p, 6q, 5q and 3p. Conclusions We present the first genome-wide analysis of the largest international series of Ollier ECs and CS reported so far and demonstrate that copy number alterations and LOH are rare and non-recurrent in Ollier ECs while secondary CS are genetically unstable. One could predict that instead small deletions, point mutations or epigenetic mechanisms play a role in the origin of ECs of Ollier disease.
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Affiliation(s)
- Twinkal C Pansuriya
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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23
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Middeldorp A, Jagmohan-Changur SC, van der Klift HM, van Puijenbroek M, Houwing-Duistermaat JJ, Webb E, Houlston R, Tops C, Vasen HFA, Devilee P, Morreau H, van Wezel T, Wijnen J. Comprehensive genetic analysis of seven large families with mismatch repair proficient colorectal cancer. Genes Chromosomes Cancer 2010; 49:539-48. [PMID: 20222047 DOI: 10.1002/gcc.20763] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
Abstract
Approximately 40% of colorectal cancer (CRC) families with a diagnosis of hereditary nonpolyposis CRC on the basis of clinical criteria are not a consequence of mismatch repair (MMR) deficiency. Such families provide supporting evidence for the existence of a hitherto unidentified highly penetrant gene mutation. To gain further understanding of MMR-competent familial colorectal cancer (FCC), we studied seven large families with an unexplained predisposition for CRC to identify genetic regions that could harbor CRC risk factors. First, we conducted a genome-wide linkage scan using 10K single-nucleotide polymorphism (SNP) arrays to search for disease loci. Second, we studied the genomic profiles of the tumors of affected family members to identify commonly altered genomic regions likely to harbor tumor suppressor genes. Finally, we studied the possible role of recently identified low-risk variants in the familial aggregation of CRC in these families. Linkage analysis did not reveal clear regions of linkage to CRC. However, our results provide support linkage to 3q, a region that has previously been linked to CRC susceptibility. Tumor profiling did not reveal any genomic regions commonly targeted in the tumors studied here. Overall, the genomic profiles of the tumors show some resemblance to sporadic CRC, but additional aberrations were also present. Furthermore, the FCC families did not appear to have an enrichment of low-risk CRC susceptibility loci. These data suggest that factors other than a highly penetrant risk factor, such as low or moderate-penetrance risk factors, may explain the increased cancer risk in a subset of familial CRCs.
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Affiliation(s)
- Anneke Middeldorp
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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24
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Navin NE, Hicks J. Tracing the tumor lineage. Mol Oncol 2010; 4:267-83. [PMID: 20537601 DOI: 10.1016/j.molonc.2010.04.010] [Citation(s) in RCA: 97] [Impact Index Per Article: 6.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2010] [Revised: 04/23/2010] [Accepted: 04/23/2010] [Indexed: 12/13/2022] Open
Abstract
Defining the pathways through which tumors progress is critical to our understanding and treatment of cancer. We do not routinely sample patients at multiple time points during the progression of their disease, and thus our research is limited to inferring progression a posteriori from the examination of a single tumor sample. Despite this limitation, inferring progression is possible because the tumor genome contains a natural history of the mutations that occur during the formation of the tumor mass. There are two approaches to reconstructing a lineage of progression: (1) inter-tumor comparisons, and (2) intra-tumor comparisons. The inter-tumor approach consists of taking single samples from large collections of tumors and comparing the complexity of the genomes to identify early and late mutations. The intra-tumor approach involves taking multiple samples from individual heterogeneous tumors to compare divergent clones and reconstruct a phylogenetic lineage. Here we discuss how these approaches can be used to interpret the current models for tumor progression. We also compare data from primary and metastatic copy number profiles to shed light on the final steps of breast cancer progression. Finally, we discuss how recent technical advances in single cell genomics will herald a new era in understanding the fundamental basis of tumor heterogeneity and progression.
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Affiliation(s)
- Nicholas E Navin
- Cold Spring Harbor Laboratory, 1 Bungtown Road, Cold Spring Harbor, NY 11724, USA.
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25
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van Eijk R, Eilers PHC, Natté R, Cleton-Jansen AM, Morreau H, van Wezel T, Oosting J. MLPAinter for MLPA interpretation: an integrated approach for the analysis, visualisation and data management of Multiplex Ligation-dependent Probe Amplification. BMC Bioinformatics 2010; 11:67. [PMID: 20113482 PMCID: PMC3098110 DOI: 10.1186/1471-2105-11-67] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2009] [Accepted: 01/29/2010] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Multiplex Ligation-Dependent Probe Amplification (MLPA) is an application that can be used for the detection of multiple chromosomal aberrations in a single experiment. In one reaction, up to 50 different genomic sequences can be analysed. For a reliable work-flow, tools are needed for administrative support, data management, normalisation, visualisation, reporting and interpretation. RESULTS Here, we developed a data management system, MLPAInter for MLPA interpretation, that is windows executable and has a stand-alone database for monitoring and interpreting the MLPA data stream that is generated from the experimental setup to analysis, quality control and visualisation. A statistical approach is applied for the normalisation and analysis of large series of MLPA traces, making use of multiple control samples and internal controls. CONCLUSIONS MLPAinter visualises MLPA data in plots with information about sample replicates, normalisation settings, and sample characteristics. This integrated approach helps in the automated handling of large series of MLPA data and guarantees a quick and streamlined dataflow from the beginning of an experiment to an authorised report.
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Affiliation(s)
- Ronald van Eijk
- Department of Pathology, Leiden University Medical Center, Leiden, The Netherlands
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Corver WE, ter Haar NT. High-resolution multiparameter DNA flow cytometry for the detection and sorting of tumor and stromal subpopulations from paraffin-embedded tissues. ACTA ACUST UNITED AC 2009; Chapter 6:Unit 6.27. [PMID: 19816924 DOI: 10.1002/0471142956.cy0627s50] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/09/2022]
Abstract
This unit contains a detailed protocol for the simultaneous flow cytometric measurement of tumor cells, stromal cells, and DNA content of formalin-fixed, paraffin-embedded (FFPE) tissues. The vimentin-positive stromal cell fraction can be used as an internal reference for DNA content assessments. This allows clear detection of keratin-positive tumor cells with a DNA index lower than 1.0 and of keratin-positive tumor cells with a DNA close to 1.0 in overall DNA aneuploid samples, thus improved DNA ploidy assessment in FFPE carcinomas. Furthermore, the protocol is useful for studying molecular genetic alterations and intratumor heterogeneity in archival FFPE samples. Keratin-positive tumor cell fractions can be flow-sorted for further molecular genetic analysis, while DNA from the sorted vimentin-positive stromal cells can serve as a reference when normal tissue of the patient is not available.
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Navin N, Krasnitz A, Rodgers L, Cook K, Meth J, Kendall J, Riggs M, Eberling Y, Troge J, Grubor V, Levy D, Lundin P, Månér S, Zetterberg A, Hicks J, Wigler M. Inferring tumor progression from genomic heterogeneity. Genome Res 2009; 20:68-80. [PMID: 19903760 DOI: 10.1101/gr.099622.109] [Citation(s) in RCA: 369] [Impact Index Per Article: 24.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/25/2022]
Abstract
Cancer progression in humans is difficult to infer because we do not routinely sample patients at multiple stages of their disease. However, heterogeneous breast tumors provide a unique opportunity to study human tumor progression because they still contain evidence of early and intermediate subpopulations in the form of the phylogenetic relationships. We have developed a method we call Sector-Ploidy-Profiling (SPP) to study the clonal composition of breast tumors. SPP involves macro-dissecting tumors, flow-sorting genomic subpopulations by DNA content, and profiling genomes using comparative genomic hybridization (CGH). Breast carcinomas display two classes of genomic structural variation: (1) monogenomic and (2) polygenomic. Monogenomic tumors appear to contain a single major clonal subpopulation with a highly stable chromosome structure. Polygenomic tumors contain multiple clonal tumor subpopulations, which may occupy the same sectors, or separate anatomic locations. In polygenomic tumors, we show that heterogeneity can be ascribed to a few clonal subpopulations, rather than a series of gradual intermediates. By comparing multiple subpopulations from different anatomic locations, we have inferred pathways of cancer progression and the organization of tumor growth.
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Affiliation(s)
- Nicholas Navin
- Cold Spring Harbor Laboratory, Cold Spring Harbor, New York 11724, USA
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