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Lawrie A, Han S, Sud A, Hosking F, Cezard T, Turner D, Clark C, Murray GI, Culligan DJ, Houlston RS, Vickers MA. Combined linkage and association analysis of classical Hodgkin lymphoma. Oncotarget 2018; 9:20377-20385. [PMID: 29755658 PMCID: PMC5945548 DOI: 10.18632/oncotarget.24872] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/07/2017] [Accepted: 03/01/2018] [Indexed: 12/29/2022] Open
Abstract
The heritability of classical Hodgkin lymphoma (cHL) has yet to be fully deciphered. We report a family with five members diagnosed with nodular sclerosis cHL. Genetic analysis of the family provided evidence of linkage at chromosomes 2q35-37, 3p14-22 and 21q22, with logarithm of odds score >2. We excluded the possibility of common genetic variation influencing cHL risk at regions of linkage, by analysing GWAS data from 2,201 cHL cases and 12,460 controls. Whole exome sequencing of affected family members identified the shared missense mutations p.(Arg76Gln) in FAM107A and p.(Thr220Ala) in SLC26A6 at 3p21 as being predicted to impact on protein function. FAM107A expression was shown to be low or absent in lymphoblastoid cell lines and SLC26A6 expression lower in lymphoblastoid cell lines derived from p.(Thr220Ala) mutation carriers. Expression of FAM107A and SLC26A6 was low or absent in Hodgkin Reed-Sternberg (HRS) cell lines and in HRS cells in Hodgkin lymphoma tissue. No sequence variants were detected in KLHDC8B, a gene previously suggested as a cause of familial cHL linked to 3p21. Our findings provide evidence for candidate gene susceptibility to familial cHL.
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Affiliation(s)
- Alastair Lawrie
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Shuo Han
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- Current address: Clinical Trials Manager, MD Anderson Cancer Centre Investigational Cancer Therapeutics, Houston, TX, USA
| | - Amit Sud
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Fay Hosking
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Timothee Cezard
- The Genepool, University of Edinburgh, Edinburgh, United Kingdom
| | - David Turner
- Scottish National Blood Transfusion Service, Edinburgh, United Kingdom
| | - Caroline Clark
- Department of Medical Genetics, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Graeme I. Murray
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
| | - Dominic J. Culligan
- Department of Haematology, Aberdeen Royal Infirmary, Aberdeen, United Kingdom
| | - Richard S. Houlston
- Division of Genetics and Epidemiology, The Institute of Cancer Research, London, UK
| | - Mark A. Vickers
- School of Medicine, Medical Sciences and Nutrition, University of Aberdeen, Aberdeen, United Kingdom
- Scottish National Blood Transfusion Service, Edinburgh, United Kingdom
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Arsuaga J, Borrman T, Cavalcante R, Gonzalez G, Park C. Identification of Copy Number Aberrations in Breast Cancer Subtypes Using Persistence Topology. MICROARRAYS (BASEL, SWITZERLAND) 2015; 4:339-69. [PMID: 27600228 PMCID: PMC4996377 DOI: 10.3390/microarrays4030339] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/09/2015] [Accepted: 08/03/2015] [Indexed: 01/01/2023]
Abstract
DNA copy number aberrations (CNAs) are of biological and medical interest because they help identify regulatory mechanisms underlying tumor initiation and evolution. Identification of tumor-driving CNAs (driver CNAs) however remains a challenging task, because they are frequently hidden by CNAs that are the product of random events that take place during tumor evolution. Experimental detection of CNAs is commonly accomplished through array comparative genomic hybridization (aCGH) assays followed by supervised and/or unsupervised statistical methods that combine the segmented profiles of all patients to identify driver CNAs. Here, we extend a previously-presented supervised algorithm for the identification of CNAs that is based on a topological representation of the data. Our method associates a two-dimensional (2D) point cloud with each aCGH profile and generates a sequence of simplicial complexes, mathematical objects that generalize the concept of a graph. This representation of the data permits segmenting the data at different resolutions and identifying CNAs by interrogating the topological properties of these simplicial complexes. We tested our approach on a published dataset with the goal of identifying specific breast cancer CNAs associated with specific molecular subtypes. Identification of CNAs associated with each subtype was performed by analyzing each subtype separately from the others and by taking the rest of the subtypes as the control. Our results found a new amplification in 11q at the location of the progesterone receptor in the Luminal A subtype. Aberrations in the Luminal B subtype were found only upon removal of the basal-like subtype from the control set. Under those conditions, all regions found in the original publication, except for 17q, were confirmed; all aberrations, except those in chromosome arms 8q and 12q were confirmed in the basal-like subtype. These two chromosome arms, however, were detected only upon removal of three patients with exceedingly large copy number values. More importantly, we detected 10 and 21 additional regions in the Luminal B and basal-like subtypes, respectively. Most of the additional regions were either validated on an independent dataset and/or using GISTIC. Furthermore, we found three new CNAs in the basal-like subtype: a combination of gains and losses in 1p, a gain in 2p and a loss in 14q. Based on these results, we suggest that topological approaches that incorporate multiresolution analyses and that interrogate topological properties of the data can help in the identification of copy number changes in cancer.
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Affiliation(s)
- Javier Arsuaga
- Department of Mathematics, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA.
- Department of Molecular and Cellular Biology, University of California Davis, 1 Shields Avenue, Davis, CA 95616, USA.
| | - Tyler Borrman
- Program in Bioinformatics and Integrative Biology, University of Massachusetts Medical School, Worcester, MA 01605, USA.
| | - Raymond Cavalcante
- Department of Computational Medicine and Bioinformatics, University of Michigan, Ann Arbor, MI 48109, USA.
| | - Georgina Gonzalez
- Department of Mathematics, San Francisco State University, 1600 Holloway Avenue, San Francisco, CA 96132, USA.
| | - Catherine Park
- Helen Diller Comprehensive Cancer Center,University of California San Francisco, 1600 Divisadero Street, San Francisco, CA 94143, USA.
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Loss of Heterozygosity in Thyroid Hormone Receptor Beta in Invasive Breast Cancer. TUMORI JOURNAL 2015; 101:572-7. [PMID: 26350179 DOI: 10.5301/tj.5000272] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 01/29/2015] [Indexed: 11/20/2022]
Abstract
Background Loss of heterozygosity (LOH) on chromosome arm 3p, where the gene of thyroid hormone receptor beta (THRB) is located, has been reported in breast cancer. Although some studies performed in vitro have suggested that THRB could act as a tumor suppressor in breast cancer development, there is still no unequivocal evidence to support this. Methods To determine the role of LOH in breast tumor development, the LOH of THRB and its proximal microsatellite markers D3S1293, D3S3659, D3S3700, D3S2307 and D3S2336 was investigated in a genomic region spanning ~3.3 Mb in tumor specimens and in corresponding normal tissues of 74 invasive breast cancer patients. The association was analyzed between LOH in microsatellite markers and clinicopathological characteristics. Results LOH was detected in D3S1293 (36.7%), THRB (59.4%), D3S3659 (37.5%) and D3S3700 (55.2%) among the informative cases, while LOH was not detected in D3S2307 and D3S2336. Cases exhibited LOH of 52.8%-71.4% if any 2 markers were combined and analyzed out of the first 4 microsatellite markers. LOH in THRB was associated with negative estrogen receptor (ER), negative progesterone receptor (PR), both negative estrogen receptor and progesterone receptor (HR) and human epidermal growth factor receptor-2 (HER2) and lymph node metastasis (p = 0.0001, p = 0.005, p = 0.001 and p = 0.018). The association with negative PR in LOH in THRB and/or D3S1293 was pronounced (p<0.0001). LOH in D3S3700 showed an association with lymph node metastasis (p = 0.014). This association was enhanced if D3S3700 was combined with THRB or D3S3659 (p = 0.0004, p = 0.0002). Conclusions LOH in THRB and its proximal microsatellite markers may play a role in tumorigenesis and development in invasive breast cancer.
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Combined analysis of copy number alterations by single-nucleotide polymorphism array and MYC status in non-metastatic breast cancer patients: comparison according to the circulating tumor cell status. Tumour Biol 2014; 36:711-8. [PMID: 25286758 DOI: 10.1007/s13277-014-2668-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2014] [Accepted: 09/22/2014] [Indexed: 10/24/2022] Open
Abstract
Recent technological advances have made it possible to detect circulating tumor cells (CTCs) as a prognostic marker in operable breast cancer patients. Whether the presence of CTCs in cancer patients correlates with molecular alterations in the primary tumor has not been widely explored. We identified 14 primary breast cancer specimens with known CTC status, in order to evaluate the presence of differential genetic aberrations by using SNP array assay. There was a global increase of altered genome, CNA, and copy-neutral loss of heterozygosity (cn-LOH) observed in the CTC-positive (CTC(+)) versus CTC-negative (CTC(-)) cases. As the preliminary results showed a higher proportion of copy number alteration (CNA) at 8q24 (MYC loci) and the available evidence supporting the role of MYC in the processes cancer metastases is conflicting, MYC status was determined in tissue microarray sections in a larger series of patients (n = 49) with known CTC status using FISH. MYC was altered in 62% (16/26) CTC(+) patients and in 43% (6/14) CTC(-) patients (p = 0.25). Based on the observation in our study, future studies involving a larger number of patients should be performed in order to definitively define if this correlation exists.
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