@article {233, title = {Co-Expression Network Analysis of Fbxw7-Associated LncRNAs Reveals Their Functions in Radiation-Induced Thymic Lymphoma.}, journal = {Insights Cancer Res}, volume = {1}, year = {2016}, month = {2016}, pages = {1-5}, abstract = {

FBXW7, an E3-ubiquitin protein ligase in SCFs (SKP1-cullin-F-box) complex, is a major human tumor suppressor gene, and understanding mechanisms by which FBXW7 contributes to tumorigenesis is critical for the treatment of human cancers with FBXW7 deficiency. Long non-coding RNAs (lncRNAs) have emerged as key regulators of various biological processes. Here we have identified a set of lncRNAs that are associated with Fbxw7 deficiency. The correlation network and functional annotation analysis revealed that Fbxw7-associated lncRNAs regulate genes involved in cell cycle, DNA repair, metabolic process, and cell communication and adhesion. The number of coding genes that correlated with individual lncRNAs varied largely. A lncRNA on chromosome 15 (A_30_P01032978), which was upregulated in tumors from Fbxw7 deficient mice was positively correlated with 15 coding genes. High expression of this 15-gene signature was associated with poor prognosis in two independent human breast cancer studies. Our results open possible new avenues to understand mechanisms by which Fbxw7 deficiency increases tumor susceptibility via the alteration of lncRNAs.

}, author = {A Snijders and Jiang-Hua Mao} } @article {231, title = {Expression profiling reveals transcriptional regulation by Fbxw7/mTOR pathway in radiation-induced mouse thymic lymphomas.}, journal = {Oncotarget}, volume = {6}, year = {2015}, month = {2015 Dec 29}, pages = {44794-805}, abstract = {

The tumor suppressor gene FBXW7 is deleted and mutated in many different types of human cancers. FBXW7 primarily exerts its tumor suppressor activity by ubiquitinating different oncoproteins including mTOR. Here we used gene transcript profiling to gain a deeper understanding of the role of FBXW7 in tumor development and to determine the influence of mTOR inhibition by rapamycin on tumor transcriptome and biological functions. In comparison to tumors from p53 single heterozygous (p53+/-) mice, we find that radiation-induced thymic lymphomas from Fbxw7/p53 double heterozygous (Fbxw7+/-p53+/-) mice show significant deregulation of cholesterol metabolic processes independent of rapamycin treatment, while cell cycle related genes were upregulated in tumors from placebo treated Fbxw7+/-p53+/- mice, but not in tumors from rapamycin treated Fbxw7+/-p53+/- mice. On the other hand, tumors from rapamycin treated Fbxw7+/-p53+/- mice were enriched for genes involved in the integrated stress response, an adaptive mechanism to survive in stressful environments. Finally, we demonstrated that the Fbxw7 gene signatures identified in mouse tumors significantly overlap with FBXW7 co-expressed genes in human cancers. Importantly these common FBXW7 gene signatures between mouse and human are predictive for disease-free survival in human colon, breast and lung adenocarcinoma cancer patients. These results provide novel insights into the role of FBXW7 in tumor development and have identified a number of potential targets for therapeutic intervention.

}, issn = {1949-2553}, doi = {10.18632/oncotarget.6328}, author = {A Snijders and Liu, Yueyong and Su, Li and Huang, Yurong and Jiang-Hua Mao} } @article {215, title = {Genetic background influences loss of heterozygosity patterns in radiation-induced mouse thymic lymphoma.}, journal = {J Nat Sci}, volume = {1}, year = {2015}, month = {2015}, pages = {e96}, abstract = {

Previous studies have revealed that p53 heterozygous (p53+/-) mice are extremely susceptible to radiation-induced tumorigenesis. To investigate whether genetic background influences radiation induced tumor susceptibility, we crossed p53+/- 129/Sv mice with genetically diverse strains to generate p53+/- F1 hybrids. The results showed that genetic background had a profound impact on tumor latency after exposure to gamma radiation, while the tumor spectrum did not change. We further characterized the thymic lymphomas that arose in the p53+/- mice by genome-wide loss of heterozygosity (LOH) analyses and found that genetic background strongly influenced the frequency of LOH and the loss of which parental allele on different chromosomes. Further research is needed to identify which genetic variations control the LOH patterns in radiation-induced thymic lymphomas and to evaluate its relevance to human cancers.

}, issn = {2377-2700}, author = {Hang, Michael and Huang, Yurong and A Snijders and Jiang-Hua Mao} } @article {214, title = {Genetic Background Modulates lncRNA-Coordinated Tissue Response to Low Dose Ionizing Radiation.}, journal = {Int J Genomics}, volume = {2015}, year = {2015}, month = {2015}, pages = {461038}, abstract = {

Long noncoding RNAs (lncRNAs) are emerging as key regulators of diverse cell functions and processes. However, the relevance of lncRNAs in the cell and tissue response to ionizing radiation has not yet been characterized. Here we used microarray profiling to determine lncRNA and mRNA expression in mammary glands of BALB/c and SPRET/EiJ mice after low-dose ionizing radiation (LDIR) exposure. We found that unirradiated mammary tissues of these strains differed significantly in baseline expressions of 290 lncRNAs. LDIR exposure (10 cGy) induced a significant change in the expression of many lncRNAs. The vast majority of lncRNAs identified to be differentially expressed after LDIR in either BALB/c or SPRET/EiJ had a significantly correlated expression pattern with at least one LDIR responsive mRNA. Functional analysis revealed that the response to LDIR in BALB/c mice is highly dynamic with enrichment for genes involved in tissue injury, inflammatory responses, and mammary gland development at 2, 4, and 8 weeks after LDIR, respectively. Our study demonstrates that genetic background strongly influences the expression of lncRNAs and their response to radiation and that lncRNAs may coordinate the tissue response to LDIR exposure via regulation of coding mRNAs.

}, issn = {2314-436X}, doi = {10.1155/2015/461038}, author = {Tang, Jonathan and Huang, Yurong and Nguyen, David H and Costes, Sylvain V and A Snijders and Jiang-Hua Mao} } @article {229, title = {Identification of genetic factors that modify motor performance and body weight using Collaborative Cross mice.}, journal = {Sci Rep}, volume = {5}, year = {2015}, month = {2015}, pages = {16247}, abstract = {

Evidence has emerged that suggests a link between motor deficits, obesity and many neurological disorders. However, the contributing genetic risk factors are poorly understood. Here we used the Collaborative Cross (CC), a large panel of newly inbred mice that captures 90\% of the known variation among laboratory mice, to identify the genetic loci controlling rotarod performance and its relationship with body weight in a cohort of 365 mice across 16 CC strains. Body weight and rotarod performance varied widely across CC strains and were significantly negatively correlated. Genetic linkage analysis identified 14 loci that were associated with body weight. However, 45 loci affected rotarod performance, seven of which were also associated with body weight, suggesting a strong link at the genetic level. Lastly, we show that genes identified in this study overlap significantly with those related to neurological disorders and obesity found in human GWA studies. In conclusion, our results provide a genetic framework for studies of the connection between body weight, the central nervous system and behavior.

}, issn = {2045-2322}, doi = {10.1038/srep16247}, author = {Jiang-Hua Mao and Langley, Sasha A and Huang, Yurong and Hang, Michael and Bouchard, Kristofer E and Celniker, Susan E and Brown, James B and Jansson, Janet K and Karpen, Gary H and A Snijders} } @article {219, title = {Identification of genetic loci that control mammary tumor susceptibility through the host microenvironment.}, journal = {Sci Rep}, volume = {5}, year = {2015}, month = {2015}, pages = {8919}, abstract = {

The interplay between host genetics, tumor microenvironment and environmental exposure in cancer susceptibility remains poorly understood. Here we assessed the genetic control of stromal mediation of mammary tumor susceptibility to low dose ionizing radiation (LDIR) using backcrossed F1 into BALB/c (F1Bx) between cancer susceptible (BALB/c) and resistant (SPRET/EiJ) mouse strains. Tumor formation was evaluated after transplantation of non-irradiated Trp53-/- BALB/c mammary gland fragments into cleared fat pads of F1Bx hosts. Genome-wide linkage analysis revealed 2 genetic loci that constitute the baseline susceptibility via host microenvironment. However, once challenged with LDIR, we discovered 13 additional loci that were enriched for genes involved in cytokines, including TGFβ1 signaling. Surprisingly, LDIR-treated F1Bx cohort significantly reduced incidence of mammary tumors from Trp53-/- fragments as well as prolonged tumor latency, compared to sham-treated controls. We demonstrated further that plasma levels of specific cytokines were significantly correlated with tumor latency. Using an ex vivo 3-D assay, we confirmed TGFβ1 as a strong candidate for reduced mammary invasion in SPRET/EiJ, which could explain resistance of this strain to mammary cancer risk following LDIR. Our results open possible new avenues to understand mechanisms of genes operating via the stroma that affect cancer risk from external environmental exposures.

}, keywords = {Animals, Breast Neoplasms, Cell Line, Tumor, Cytokines, Female, Genetic Predisposition to Disease, Mice, Mice, Inbred BALB C, Neoplasms, Radiation-Induced, Quantitative Trait Loci, Risk Factors, Transforming Growth Factor beta1, Tumor Microenvironment}, issn = {2045-2322}, doi = {10.1038/srep08919}, author = {Zhang, Pengju and Lo, Alvin and Huang, Yurong and Huang, Ge and Liang, Guozhou and Mott, Joni and Karpen, Gary H and Blakely, Eleanor A and Bissell, Mina J and Barcellos-Hoff, Mary Helen and A Snijders and Jiang-Hua Mao} } @article {222, title = {Low-dose radiation cancer susceptibility models.}, journal = {Aging (Albany NY)}, volume = {7}, year = {2015}, month = {2015 Jun}, pages = {352-3}, keywords = {Dose-Response Relationship, Radiation, Genetic Predisposition to Disease, Humans, Models, Biological, Neoplasms, Radiation-Induced, Risk Factors}, issn = {1945-4589}, doi = {10.18632/aging.100767}, author = {Jiang-Hua Mao and A Snijders} } @article {282, title = {Micronucleus formation in human keratinocytes is dependent on radiation quality and tissue architecture.}, journal = {Environ Mol Mutagen}, volume = {56}, year = {2015}, month = {2015 Jan}, pages = {22-31}, abstract = {

The cytokinesis-block micronucleus (MN) assay was used to assess the genotoxicity of low doses of different types of space radiation. Normal human primary keratinocytes and immortalized keratinocytes grown in 2D monolayers each were exposed to graded doses of 0.3 or 1.0 GeV/n silicon ions or similar energies of iron ions. The frequencies of induced MN were determined and compared to γ-ray data. RBE(max) values ranged from 1.6 to 3.9 for primary keratinocytes and from 2.4 to 6.3 for immortalized keratinocytes. At low radiation doses <= 0.4 Gy, 0.3 GeV/n iron ions were the most effective at inducing MN in normal keratinocytes. An "over-kill effect" was observed for 0.3 GeV/n iron ions at higher doses, wherein 1.0 GeV/n iron ions were most efficient in inducing MN. In immortalized keratinocytes, 0.3 GeV/n iron ions produced MN with greater frequency than 1.0 GeV/n iron ions, except at the highest dose tested. MN formation was higher in immortalized keratinocytes than in normal keratinocytes for all doses and radiation qualities investigated. MN induction was also assessed in human keratinocytes cultured in 3D to simulate the complex architecture of human skin. RBE values for MN formation in 3D were reduced for normal keratinocytes exposed to iron ions, but were elevated for immortalized keratinocytes. Overall, MN induction was significantly lower in keratinocytes cultured in 3D than in 2D. Together, the results suggest that tissue architecture and immortalization status modulate the genotoxic response to space radiation, perhaps via alterations in DNA repair fidelity.

}, keywords = {Cell Culture Techniques, Cell Proliferation, Cytokinesis, Dose-Response Relationship, Radiation, Epidermis, Fibroblasts, Gamma Rays, Humans, Immunoenzyme Techniques, Infant, Newborn, Keratinocytes, Micronuclei, Chromosome-Defective, Micronucleus Tests}, issn = {1098-2280}, doi = {10.1002/em.21887}, author = {A Snijders and Mannion, Brandon J and Leung, Stanley G and Moon, Sol C and Kronenberg, Amy and Wiese, Claudia} } @article {283, title = {Understanding cancer development processes after HZE-particle exposure: roles of ROS, DNA damage repair and inflammation.}, journal = {Radiat Res}, volume = {183}, year = {2015}, month = {2015 Jan}, pages = {1-26}, abstract = {

During space travel astronauts are exposed to a variety of radiations, including galactic cosmic rays composed of high-energy protons and high-energy charged (HZE) nuclei, and solar particle events containing low- to medium-energy protons. Risks from these exposures include carcinogenesis, central nervous system damage and degenerative tissue effects. Currently, career radiation limits are based on estimates of fatal cancer risks calculated using a model that incorporates human epidemiological data from exposed populations, estimates of relative biological effectiveness and dose-response data from relevant mammalian experimental models. A major goal of space radiation risk assessment is to link mechanistic data from biological studies at NASA Space Radiation Laboratory and other particle accelerators with risk models. Early phenotypes of HZE exposure, such as the induction of reactive oxygen species, DNA damage signaling and inflammation, are sensitive to HZE damage complexity. This review summarizes our current understanding of critical areas within the DNA damage and oxidative stress arena and provides insight into their mechanistic interdependence and their usefulness in accurately modeling cancer and other risks in astronauts exposed to space radiation. Our ultimate goals are to examine potential links and crosstalk between early response modules activated by charged particle exposure, to identify critical areas that require further research and to use these data to reduced uncertainties in modeling cancer risk for astronauts. A clearer understanding of the links between early mechanistic aspects of high-LET response and later surrogate cancer end points could reveal key nodes that can be therapeutically targeted to mitigate the health effects from charged particle exposures.

}, keywords = {Animals, Carcinogenesis, Cosmic Radiation, DNA Damage, DNA Repair, Environmental Exposure, Humans, Inflammation, Neoplasms, Radiation-Induced, Reactive Oxygen Species}, issn = {1938-5404}, doi = {10.1667/RR13804.1}, author = {Sridharan, D M and Asaithamby, A and Bailey, S M and Costes, S V and Doetsch, P W and Dynan, W S and Kronenberg, A and Rithidech, K N and Saha, J and A Snijders and Werner, E and Wiese, C and Cucinotta, F A and Pluth, J M} } @article {209, title = {An interferon signature identified by RNA-sequencing of mammary tissues varies across the estrous cycle and is predictive of metastasis-free survival.}, journal = {Oncotarget}, volume = {5}, year = {2014}, month = {2014 Jun 30}, pages = {4011-25}, abstract = {

The concept that a breast cancer patient{\textquoteright}s menstrual stage at the time of tumor surgery influences risk of metastases remains controversial. The scarcity of comprehensive molecular studies of menstrual stage-dependent fluctuations in the breast provides little insight in this observation. To gain a deeper understanding of the biological changes in mammary tissue and blood during the menstrual cycle and to determine the influence of environmental exposures, such as low-dose ionizing radiation (LDIR), we used the mouse to characterize estrous-cycle variations in mammary gene transcripts by RNA-sequencing, peripheral white blood cell (WBC) counts and plasma cytokine levels. We identified an estrous-variable and hormone-dependent gene cluster enriched for Type-1 interferon genes. Cox regression identified a 117-gene signature of interferon-associated genes, which correlated with lower frequencies of metastasis in breast cancer patients. LDIR (10cGy) exposure had no detectable effect on mammary transcripts. However, peripheral WBC counts varied across the estrous cycle and LDIR exposure reduced lymphocyte counts and cytokine levels in tumor-susceptible mice. Our finding of variations in mammary Type-1 interferon and immune functions across the estrous cycle provides a mechanism by which timing of breast tumor surgery during the menstrual cycle may have clinical relevance to a patient{\textquoteright}s risk for distant metastases.

}, keywords = {Animals, Disease-Free Survival, Estrous Cycle, Female, Humans, Interferons, Mice, Mice, Inbred BALB C, Mice, Inbred C57BL, Neoplasm Metastasis, RNA, Messenger}, issn = {1949-2553}, doi = {10.18632/oncotarget.2148}, author = {A Snijders and Langley, Sasha and Jiang-Hua Mao and Bhatnagar, Sandhya and Bjornstad, Kathleen A and Rosen, Chris J and Lo, Alvin and Huang, Yurong and Blakely, Eleanor A and Karpen, Gary H and Bissell, Mina J and Wyrobek, Andrew J} } @article {281, title = {Nanosensor dosimetry of mouse blood proteins after exposure to ionizing radiation.}, journal = {Sci Rep}, volume = {3}, year = {2013}, month = {2013}, pages = {2234}, abstract = {

Giant magnetoresistive (GMR) nanosensors provide a novel approach for measuring protein concentrations in blood for medical diagnosis. Using an in vivo mouse radiation model, we developed protocols for measuring Flt3 ligand (Flt3lg) and serum amyloid A1 (Saa1) in small amounts of blood collected during the first week after X-ray exposures of sham, 0.1, 1, 2, 3, or 6 Gy. Flt3lg concentrations showed excellent dose discrimination at >= 1 Gy in the time window of 1 to 7 days after exposure except 1 Gy at day 7. Saa1 dose response was limited to the first two days after exposure. A multiplex assay with both proteins showed improved dose classification accuracy. Our magneto-nanosensor assay demonstrates the dose and time responses, low-dose sensitivity, small volume requirements, and rapid speed that have important advantages in radiation triage biodosimetry.

}, keywords = {Animals, Biomarkers, Biosensing Techniques, Blood Proteins, Dose-Response Relationship, Radiation, Female, Male, Membrane Proteins, Mice, Nanotechnology, Radiation, Ionizing, Radiometry, Reproducibility of Results, Serum Amyloid A Protein, Time Factors}, issn = {2045-2322}, doi = {10.1038/srep02234}, author = {Kim, Dokyoon and Marchetti, Francesco and Chen, Zuxiong and Zaric, Sasa and Wilson, Robert J and Hall, Drew A and Gaster, Richard S and Lee, Jung-Rok and Wang, Junyi and Osterfeld, Sebastian J and Yu, Heng and White, Robert M and Blakely, William F and Peterson, Leif E and Bhatnagar, Sandhya and Mannion, Brandon and Tseng, Serena and Roth, Kristen and Coleman, Matthew and A Snijders and Wyrobek, Andrew J and Wang, Shan X} } @article {280, title = {DNA repair and cell cycle biomarkers of radiation exposure and inflammation stress in human blood.}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e48619}, abstract = {

DNA damage and repair are hallmarks of cellular responses to ionizing radiation. We hypothesized that monitoring the expression of DNA repair-associated genes would enhance the detection of individuals exposed to radiation versus other forms of physiological stress. We employed the human blood ex vivo radiation model to investigate the expression responses of DNA repair genes in repeated blood samples from healthy, non-smoking men and women exposed to 2 Gy of X-rays in the context of inflammation stress mimicked by the bacterial endotoxin lipopolysaccharide (LPS). Radiation exposure significantly modulated the transcript expression of 12 genes of 40 tested (2.2E-06

}, keywords = {Adult, Biomarkers, Cell Cycle, DNA Repair, Dose-Response Relationship, Radiation, Female, Gene Expression Regulation, Humans, Inflammation, Lipopolysaccharides, Male, Middle Aged, Phosphorylation, Predictive Value of Tests, Reproducibility of Results, RNA, Messenger, Stress, Physiological, Time Factors, Transcription, Genetic, X-Rays, Young Adult}, issn = {1932-6203}, doi = {10.1371/journal.pone.0048619}, author = {Budworth, Helen and A Snijders and Marchetti, Francesco and Mannion, Brandon and Bhatnagar, Sandhya and Kwoh, Ely and Tan, Yuande and Wang, Shan X and Blakely, William F and Coleman, Matthew and Peterson, Leif and Wyrobek, Andrew J} } @article {78, title = {Genetic differences in transcript responses to low-dose ionizing radiation identify tissue functions associated with breast cancer susceptibility}, journal = {PLoS One}, volume = {7}, year = {2012}, month = {2012}, pages = {e45394}, abstract = {

High dose ionizing radiation (IR) is a well-known risk factor for breast cancer but the health effects after low-dose (LD, \<10 cGy) exposures remain highly uncertain. We explored a systems approach that compared LD-induced chromosome damage and transcriptional responses in strains of mice with genetic differences in their sensitivity to radiation-induced mammary cancer (BALB/c and C57BL/6) for the purpose of identifying mechanisms of mammary cancer susceptibility. Unirradiated mammary and blood tissues of these strains differed significantly in baseline expressions of DNA repair, tumor suppressor, and stress response genes. LD exposures of 7.5 cGy (weekly for 4 weeks) did not induce detectable genomic instability in either strain. However, the mammary glands of the sensitive strain but not the resistant strain showed early transcriptional responses involving: (a) diminished immune response, (b) increased cellular stress, (c) altered TGFβ-signaling, and (d) inappropriate expression of developmental genes. One month after LD exposure, the two strains showed opposing responses in transcriptional signatures linked to proliferation, senescence, and microenvironment functions. We also discovered a pre-exposure expression signature in both blood and mammary tissues that is predictive for poor survival among human cancer patients (p = 0.0001), and a post-LD-exposure signature also predictive for poor patient survival (p\<0.0001). There is concordant direction of expression in the LD-exposed sensitive mouse strain, in biomarkers of human DCIS and in biomarkers of human breast tumors. Our findings support the hypothesis that genetic mechanisms that determine susceptibility to LD radiation induced mammary cancer in mice are similar to the tissue mechanisms that determine poor-survival in breast cancer patients. We observed non-linearity of the LD responses providing molecular evidence against the LNT risk model and obtained new evidence that LD responses are strongly influenced by genotype. Our findings suggest that the biological assumptions concerning the mechanisms by which LD radiation is translated into breast cancer risk should be reexamined and suggest a new strategy to identify genetic features that predispose or protect individuals from LD-induced breast cancer.

}, keywords = {Animals, Breast Neoplasms, Dose-Response Relationship, Radiation, Female, Genetic Predisposition to Disease, Genomic Instability, Humans, Mice, Mice, Inbred BALB C, Mice, Inbred C57BL, Radiation, Ionizing, RNA, Messenger, Survival Analysis, Transcription, Genetic, Tumor Microenvironment}, issn = {1932-6203}, doi = {10.1371/journal.pone.0045394}, author = {A Snijders and Marchetti, Francesco and Bhatnagar, Sandhya and Duru, Nadire and Ju Han and Hu, Zhi and Jiang-Hua Mao and Gray, Joe W and Wyrobek, Andrew J} } @article {279, title = {Two distinct routes to oral cancer differing in genome instability and risk for cervical node metastasis.}, journal = {Clin Cancer Res}, volume = {17}, year = {2011}, month = {2011 Nov 15}, pages = {7024-34}, abstract = {

PURPOSE: Problems in management of oral cancers or precancers include identification of patients at risk for metastasis, tumor recurrence, and second primary tumors or risk for progression of precancers (dysplasia) to cancer. Thus, the objective of this study was to clarify the role of genomic aberrations in oral cancer progression and metastasis.

EXPERIMENTAL DESIGN: The spectrum of copy number alterations in oral dysplasia and squamous cell carcinomas (SCC) was determined by array comparative genomic hybridization. Associations with clinical characteristics were studied and results confirmed in an independent cohort.

RESULTS: The presence of one or more of the chromosomal aberrations +3q24-qter, -8pter-p23.1, +8q12-q24.2, and +20 distinguishes a major subgroup (70\%-80\% of lesions, termed 3q8pq20 subtype) from the remainder (20\%-30\% of lesions, non-3q8pq20). The 3q8pq20 subtype is associated with chromosomal instability and differential methylation in the most chromosomally unstable tumors. The two subtypes differ significantly in clinical outcome with risk for cervical (neck) lymph node metastasis almost exclusively associated with the 3q8pq20 subtype in two independent oral SCC cohorts.

CONCLUSIONS: Two subtypes of oral lesions indicative of at least two pathways for oral cancer development were distinguished that differ in chromosomal instability and risk for metastasis, suggesting that +3q,-8p, +8q, and +20 constitute a biomarker with clinical utility for identifying patients at risk for metastasis. Moreover, although increased numbers of genomic alterations can be harbingers of progression to cancer, dysplastic lesions lacking copy number changes cannot be considered benign as they are potential precursors to non-3q8pq20 locally invasive, yet not metastatic oral SCC.

}, keywords = {Carcinoma, Squamous Cell, Cohort Studies, Comparative Genomic Hybridization, Disease Progression, DNA Copy Number Variations, Female, Genomic Instability, Head and Neck Neoplasms, Humans, Lymphatic Metastasis, Male, Middle Aged, Mouth Neoplasms, Precancerous Conditions, Risk}, issn = {1078-0432}, doi = {10.1158/1078-0432.CCR-11-1944}, author = {Bhattacharya, Aditi and Roy, Ritu and A Snijders and Hamilton, Gregory and Paquette, Jesse and Tokuyasu, Taku and Bengtsson, Henrik and Jordan, Richard C K and Olshen, Adam B and Pinkel, Daniel and Schmidt, Brian L and Albertson, Donna G} } @article {278, title = {Array comparative genomic hybridization analysis indicates that serous carcinomas of the ovary, fallopian tube and endometrium are distinct entities.}, journal = {Histopathology}, volume = {57}, year = {2010}, month = {2010 Oct}, pages = {634-7}, keywords = {Biomarkers, Tumor, Chromosomes, Artificial, Bacterial, Comparative Genomic Hybridization, Cystadenocarcinoma, Serous, Endometrial Neoplasms, Fallopian Tube Neoplasms, Female, Gene Expression Profiling, Humans, Microarray Analysis, Ovarian Neoplasms}, issn = {1365-2559}, doi = {10.1111/j.1365-2559.2010.03656.x}, author = {Nowee, Marlies E and Seeber, Laura Ms and Horr{\'e}e, Nicole and A Snijders and van Diest, Paul J and Verheijen, Ren{\'e} Hm and Dorsman, Josephine C} } @article {277, title = {Genomic profiling by array comparative genomic hybridization reveals novel DNA copy number changes in breast phyllodes tumours.}, journal = {Cell Oncol}, volume = {31}, year = {2009}, month = {2009}, pages = {31-9}, abstract = {

Breast phyllodes tumour (PT) is a rare fibroepithelial tumour. The genetic alterations contributing to its tumorigenesis are largely unknown. To identify genomic regions involved in pathogenesis and progression of PTs we obtained genome-wide copy number profiles by array comparative genomic hybridization (CGH).DNA was isolated from fresh-frozen tissue samples. 11 PTs and 3 fibroadenomas, a frequently occurring fibroepithelial breast tumour, were analyzed. Arrays composed of 2464 genomic clones were used, providing a resolution of ~1.4 Mb across the genome. Each clone contains at least one STS for linkage to the human genome sequence.No copy number changes were detected in fibroadenomas. On the other hand, 10 of 11 PT (91\%) showed DNA copy number alterations. The mean number of chromosomal events in PT was 5.5 (range 0-16) per case. A mean of 2.0 gains (range 0-10) and 3.0 losses (range 0-9) was seen per case of PT. Three cases showed amplifications. DNA copy number change was not related to PT grade. We observed recurrent loss on chromosome 1q, 4p, 10, 13q, 15q, 16, 17p, 19 and X. Recurrent copy number gain was seen on 1q, 2p, 3q, 7p, 8q, 16q, 20.In this study we used array CGH for genomic profiling of fibroepithelial breast tumours. Whereas most PT showed chromosomal instability, fibroadenomas lacked copy number changes. Some copy number aberrations had not previously been associated with PT. Several well-known cancer related genes, such as TP53 and members of the Cadherin, reside within the recurrent regions of copy number alteration. Since copy number change was found in all benign PT, genomic instability may be an early event in PT genesis.

}, keywords = {Breast Neoplasms, Chromosomes, Human, Comparative Genomic Hybridization, Female, Gene Dosage, Gene Expression Profiling, Genome, Human, Humans, Oligonucleotide Array Sequence Analysis, Phyllodes Tumor}, issn = {1875-8606}, author = {Kuijper, Arno and A Snijders and Berns, Els M J J and Kuenen-Boumeester, Vibeke and van der Wall, Elsken and Albertson, Donna G and van Diest, Paul J} } @article {276, title = {Stromal control of oncogenic traits expressed in response to the overexpression of GLI2, a pleiotropic oncogene.}, journal = {Oncogene}, volume = {28}, year = {2009}, month = {2009 Feb 5}, pages = {625-37}, abstract = {

Hedgehog signaling is often activated in tumors, yet it remains unclear how GLI2, a transcription factor activated by this pathway, acts as an oncogene. We show that GLI2 is a pleiotropic oncogene. The overexpression induces genomic instability and blocks differentiation, likely mediated in part by enhanced expression of the stem cell gene SOX2. GLI2 also induces transforming growth factor (TGF)B1-dependent transdifferentiation of foreskin and tongue, but not gingival fibroblasts into myofibroblasts, creating an environment permissive for invasion by keratinocytes, which are in various stages of differentiation having downregulated GLI2. Thus, upregulated GLI2 expression is sufficient to induce a number of the acquired characteristics of tumor cells; however, the stroma, in a tissue-specific manner, determines whether certain GLI2 oncogenic traits are expressed.

}, keywords = {Adolescent, Adult, Cell Differentiation, Cell Proliferation, Cell Transformation, Neoplastic, Cells, Cultured, Gene Amplification, Genomic Instability, Humans, Keratinocytes, Kruppel-Like Transcription Factors, Neoplasms, Nuclear Proteins, Oncogenes, Organ Specificity, Stromal Cells, Up-Regulation, Young Adult}, issn = {1476-5594}, doi = {10.1038/onc.2008.421}, author = {A Snijders and Huey, B and Connelly, S T and Roy, R and Jordan, R C K and Schmidt, B L and Albertson, D G} } @article {275, title = {Acquired genomic aberrations associated with methotrexate resistance vary with background genomic instability.}, journal = {Genes Chromosomes Cancer}, volume = {47}, year = {2008}, month = {2008 Jan}, pages = {71-83}, abstract = {

Tumors vary widely in chromosomal level genome instability. To gain a better understanding of the underlying defects which foster specific types of aberrations, we investigated the response of cells of related genetic backgrounds to challenge with methotrexate. We studied mismatch repair deficient HCT116 cells, two derivatives also deficient in XRCC5 (HCT116 Ku86+/-) or BLM (HCT116 BLM-/-), and mismatch repair competent HCT116+chr3 cells. We show that colony formation occurred at a significantly higher frequency in HCT116 cells and HCT116 Ku86+/- cells compared to HCT116 BLM-/- and HCT116+chr3 cells. Visible colonies arose most rapidly in HCT116 Ku86+/- cells, whereas they formed most slowly in HCT116+chr3 cells. Copy number changes acquired by the methotrexate resistant HCT116 and HCT116 BLM-/- cells most often included whole chromosome gains or losses or no acquired copy number changes, whereas resistance in HCT116+chr3 and HCT116 Ku86+/- cells was associated with amplification of DHFR and copy number transitions leading to increased copy number of DHFR, respectively. The additional copies of DHFR were present on unstable chromosomes and organized as inverted repeats in HCT116+chr3 cells, while they were most often present as direct repeats in HCT116 Ku86+/- cells. These observations suggest that different mutational mechanisms promote drug resistance in these genetic backgrounds; mismatch repair deficiency in HCT116, high rates of chromosomal instability in HCT116 Ku86+/-, and low rates of chromosomal instability in HCT116+chr3. On the other hand, it appears that loss of BLM function suppresses the mismatch repair mutator mechanism in mismatch repair and BLM deficient HCT116 BLM-/- cells.

}, keywords = {Adenosine Triphosphatases, Antigens, Nuclear, Antimetabolites, Antineoplastic, Base Pair Mismatch, DNA Helicases, DNA-Binding Proteins, Drug Resistance, Neoplasm, Genome, Human, Genomic Instability, HCT116 Cells, Humans, Methotrexate, RecQ Helicases}, issn = {1045-2257}, doi = {10.1002/gcc.20509}, author = {A Snijders and Hermsen, Mario A and Baughman, Joshua and Buffart, Tineke E and Huey, Bing and Gajduskova, Pavla and Roydasgupta, Ritu and Tokuyasu, Taku and Meijer, Gerrit A and Fridlyand, Jane and Albertson, Donna G} } @article {273, title = {FBXW7 and DNA copy number instability.}, journal = {Breast Cancer Res Treat}, volume = {109}, year = {2008}, month = {2008 May}, pages = {47-54}, abstract = {

SKP1-cullin-F-box protein (SCF) type ubiquitin ligases degrade proteins controlling the G1/S transition. Deficiency for FBXW7 (also known as hCDC4), which encodes the F-box protein of the SCF type ubiquitin ligase is associated with genomic instability. Here, we investigated the association of FBXW7 deficiency with chromosomal instability in breast cancer. We screened 49 tumors previously profiled by array CGH for mutations in conserved regions of FBXW7, but found no mutations. Copy number loss of FBXW7, however was associated with enhanced genomic instability in the Complex breast tumor subtype, but instability may not be due to FBXW7 haploinsufficiency, since transcript levels were not reduced in tumors with loss of the locus, whereas reduced expression was observed for other neighboring genes involved in maintenance of genome stability. We also investigated whether cells deficient for FBXW7 showed enhanced instability by challenging cells with methotrexate and assessing numbers of genomic alterations arising in resistant cells. Although methotrexate resistant colonies formed at high frequencies in HCT116 FBXW7+/- and HCT116 FBXW7-/- cells compared to parental HCT116, few copy number alterations were detected in the resistant cells. Taken together these studies suggest that FBXW7 deficiency is unlikely to contribute to the extensive copy number aberrations associated with breast and possibly other tumor types.

}, keywords = {Breast Neoplasms, Cell Cycle Proteins, Cell Line, Tumor, Chromosomal Instability, Disease Progression, DNA, Drug Resistance, Neoplasm, Exons, F-Box Proteins, Genetic Techniques, Genomic Instability, Humans, Methotrexate, Mutation, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Ubiquitin-Protein Ligases}, issn = {0167-6806}, doi = {10.1007/s10549-007-9623-7}, author = {Byrd, Kristin N and Huey, Bing and Roydasgupta, Ritu and Fridlyand, Jane and A Snijders and Albertson, Donna G} } @article {274, title = {DNA profiling of primary serous ovarian and fallopian tube carcinomas with array comparative genomic hybridization and multiplex ligation-dependent probe amplification.}, journal = {J Pathol}, volume = {213}, year = {2007}, month = {2007 Sep}, pages = {46-55}, abstract = {

Primary serous ovarian carcinoma (OVCA) and serous Fallopian tube carcinoma (FTC), both belonging to the BRCA-linked tumour spectrum, share many properties and are treated similarly. However, a detailed molecular comparison has been lacking. We hypothesized that comparative genomic studies of serous OVCAs and FTCs should point to gene regions critically involved in their tumorigenesis. Array comparative genomic hybridization (array CGH) analysis indicated that serous OVCAs and serous FTCs displayed common but also more distinctive patterns of recurrent changes. Targeted gene identification using a dedicated multiplex ligation-dependent probe amplification (MLPA) probe set directly identified EIF2C2 on 8q as a potentially important driver gene. Other previously unappreciated gained/amplified genes included PSMB4 on 1q, MTSS1 on 8q, TEAD4 and TSPAN9 on 12p, and BCAS4 on 20q. SPINT2 and ACTN4 on 19q were predominantly found in FTCs. Gains/amplifications of CCNE1 and MYC, often in conjunction with changes in genes of the AKT pathway, EVI1 and PTK2, seemed to be involved at earlier stages, whereas changes of ERBB2 were associated with advanced stages. The only BRCA1-mutated FTC shared common denominators with the sporadic tumours. In conclusion, the data suggest that serous OVCAs and FTCs, although related, exhibit differences in genomic profiles. In addition to known pathways, new genes/pathways are likely to be involved, with changes in an miRNA-associated gene, EIF2C2, as one important new feature. Dedicated MLPA sets constitute potentially important tools for differential diagnosis and may provide footholds for tailored therapy.

}, keywords = {Base Sequence, Carcinoma, Cystadenocarcinoma, Serous, DNA Fingerprinting, DNA Probes, Fallopian Tube Neoplasms, Female, Gene Expression Regulation, Neoplastic, Humans, Molecular Sequence Data, Nucleic Acid Amplification Techniques, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Ovarian Neoplasms}, issn = {0022-3417}, doi = {10.1002/path.2217}, author = {Nowee, M E and A Snijders and Rockx, D A P and de Wit, R M and Kosma, V M and H{\"a}m{\"a}l{\"a}inen, K and Schouten, J P and Verheijen, R H M and van Diest, P J and Albertson, D G and Dorsman, J C} } @article {272, title = {Genome position and gene amplification.}, journal = {Genome Biol}, volume = {8}, year = {2007}, month = {2007}, pages = {R120}, abstract = {

BACKGROUND: Amplifications, regions of focal high-level copy number change, lead to overexpression of oncogenes or drug resistance genes in tumors. Their presence is often associated with poor prognosis; however, the use of amplification as a mechanism for overexpression of a particular gene in tumors varies. To investigate the influence of genome position on propensity to amplify, we integrated a mutant form of the gene encoding dihydrofolate reductase into different positions in the human genome, challenged cells with methotrexate and then studied the genomic alterations arising in drug resistant cells.

RESULTS: We observed site-specific differences in methotrexate sensitivity, amplicon organization and amplification frequency. One site was uniquely associated with a significantly enhanced propensity to amplify and recurrent amplicon boundaries, possibly implicating a rare folate-sensitive fragile site in initiating amplification. Hierarchical clustering of gene expression patterns and subsequent gene enrichment analysis revealed two clusters differing significantly in expression of MYC target genes independent of integration site.

CONCLUSION: These studies suggest that genome context together with the particular challenges to genome stability experienced during the progression to cancer contribute to the propensity to amplify a specific oncogene or drug resistance gene, whereas the overall functional response to drug (or other) challenge may be independent of the genomic location of an oncogene.

}, keywords = {Cell Line, Tumor, Gene Amplification, Gene Expression Regulation, Neoplastic, Humans, Methotrexate, Tetrahydrofolate Dehydrogenase}, issn = {1474-760X}, doi = {10.1186/gb-2007-8-6-r120}, author = {Gajduskova, Pavla and A Snijders and Kwek, Serena and Roydasgupta, Ritu and Fridlyand, Jane and Tokuyasu, Taku and Pinkel, Daniel and Albertson, Donna G} } @article {269, title = {Breast tumor copy number aberration phenotypes and genomic instability.}, journal = {BMC Cancer}, volume = {6}, year = {2006}, month = {2006}, pages = {96}, abstract = {

BACKGROUND: Genomic DNA copy number aberrations are frequent in solid tumors, although the underlying causes of chromosomal instability in tumors remain obscure. Genes likely to have genomic instability phenotypes when mutated (e.g. those involved in mitosis, replication, repair, and telomeres) are rarely mutated in chromosomally unstable sporadic tumors, even though such mutations are associated with some heritable cancer prone syndromes.

METHODS: We applied array comparative genomic hybridization (CGH) to the analysis of breast tumors. The variation in the levels of genomic instability amongst tumors prompted us to investigate whether alterations in processes/genes involved in maintenance and/or manipulation of the genome were associated with particular types of genomic instability.

RESULTS: We discriminated three breast tumor subtypes based on genomic DNA copy number alterations. The subtypes varied with respect to level of genomic instability. We find that shorter telomeres and altered telomere related gene expression are associated with amplification, implicating telomere attrition as a promoter of this type of aberration in breast cancer. On the other hand, the numbers of chromosomal alterations, particularly low level changes, are associated with altered expression of genes in other functional classes (mitosis, cell cycle, DNA replication and repair). Further, although loss of function instability phenotypes have been demonstrated for many of the genes in model systems, we observed enhanced expression of most genes in tumors, indicating that over expression, rather than deficiency underlies instability.

CONCLUSION: Many of the genes associated with higher frequency of copy number aberrations are direct targets of E2F, supporting the hypothesis that deregulation of the Rb pathway is a major contributor to chromosomal instability in breast tumors. These observations are consistent with failure to find mutations in sporadic tumors in genes that have roles in maintenance or manipulation of the genome.

}, keywords = {Adult, Aged, Breast Neoplasms, Carcinoma, Ductal, Breast, Chromosome Aberrations, Chromosomes, Human, DNA, Neoplasm, E2F Transcription Factors, Female, Gene Dosage, Gene Expression Regulation, Neoplastic, Genes, p53, Genes, Retinoblastoma, Genomic Instability, Humans, Karyotyping, Middle Aged, Neoplasm Proteins, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Phenotype, Retinoblastoma Protein, Signal Transduction, Telomere}, issn = {1471-2407}, doi = {10.1186/1471-2407-6-96}, author = {Fridlyand, Jane and A Snijders and Ylstra, Bauke and Li, Hua and Olshen, Adam and Segraves, Richard and Dairkee, Shanaz and Tokuyasu, Taku and Ljung, Britt Marie and Jain, Ajay N and McLennan, Jane and Ziegler, John and Chin, Koei and Devries, Sandy and Feiler, Heidi and Gray, Joe W and Waldman, Frederic and Pinkel, Daniel and Albertson, Donna G} } @article {271, title = {Chromosomal instability in microsatellite-unstable and stable colon cancer.}, journal = {Clin Cancer Res}, volume = {12}, year = {2006}, month = {2006 Nov 1}, pages = {6379-85}, abstract = {

PURPOSE: The genomic instability in colon cancer can be divided into at least two major types, microsatellite instability (MSI) or chromosomal instability (CIN). Although initially felt to be mutually exclusive, recent evidence suggests that there may be overlap between the two. The aim of this study was to identify chromosomal alterations at high resolution in sporadic colon cancers with high-level microsatellite instability (MSI-H) and to compare them to those present in a set of matched microsatellite stable (MSS) tumors.

EXPERIMENTAL DESIGN: Array-based comparative genomic hybridization was used to analyze a set of 23 sporadic MSI-H and 23 MSS colon cancers matched for location, gender, stage, and age. The arrays consisted of 2,464 bacterial artificial chromosome clones.

RESULTS: MSI and MSS colon cancers differed significantly with respect to frequency and type of chromosomal alterations. The median fraction of genome altered was lower among MSI-H tumors than MSS tumors (2.8\% versus 30.7\%, P=0.00006). However, the MSI-H tumors displayed a range of genomic alterations, from the absence of detectable alterations to extensive alterations. Frequent alterations in MSI-H tumors included gains of chromosomes 8, 12, and 13, and loss of 15q14. In contrast, the most frequent alterations in MSS tumors were gains of 7, 13, 8q, and 20, and losses of 8p, 17p, and 18. A small, previously uncharacterized, genomic deletion on 16p13.2, found in 35\% of MSI-H and 21\% of MSS tumors, was confirmed by fluorescence in situ hybridization.

CONCLUSION: MSI and CIN are not mutually exclusive forms of genomic instability in sporadic colon cancer, with MSI tumors also showing varying degrees of CIN.

}, keywords = {Adenocarcinoma, Aged, Aged, 80 and over, Chromosomal Instability, Colonic Neoplasms, Female, Humans, In Situ Hybridization, Fluorescence, Male, Microsatellite Instability, Middle Aged, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis}, issn = {1078-0432}, doi = {10.1158/1078-0432.CCR-06-1248}, author = {Trautmann, Karolin and Terdiman, Jonathan P and French, Amy J and Roydasgupta, Ritu and Sein, Nancy and Kakar, Sanjay and Fridlyand, Jane and A Snijders and Albertson, Donna G and Thibodeau, Stephen N and Waldman, Frederic M} } @article {268, title = {Genomic analysis of tumors by array comparative genomic hybridization: more is better.}, journal = {Cancer Res}, volume = {66}, year = {2006}, month = {2006 Apr 1}, pages = {3955-6; author reply 3956}, keywords = {Carcinoma, Squamous Cell, Cyclin-Dependent Kinase 6, Genes, erbB-1, Humans, Mouth Neoplasms, Nucleic Acid Hybridization}, issn = {0008-5472}, doi = {10.1158/0008-5472.CAN-05-3611}, author = {Albertson, Donna G and A Snijders and Fridlyand, Jane and Jordan, Richard and Pinkel, Daniel and Schmidt, Brian L} } @article {270, title = {Increased gene copy numbers at chromosome 20q are frequent in both squamous cell carcinomas and adenocarcinomas of the cervix.}, journal = {J Pathol}, volume = {209}, year = {2006}, month = {2006 Jun}, pages = {220-30}, abstract = {

Genome-wide microarray-based comparative genomic hybridization (array CGH) was used to identify common chromosomal alterations involved in cervical carcinogenesis as a first step towards the discovery of novel biomarkers. The genomic profiles of nine squamous cell carcinomas (SCCs) and seven adenocarcinomas (AdCAs), as well as four human papillomavirus (HPV)-immortalized keratinocyte cell lines, were assessed. On a genome-wide scale, SCCs showed significantly more gains than AdCAs. More specifically, there was a striking and highly significant difference between the two histological types for gain at 3q12.1-28, which was predominantly observed in SCC. Other frequent alterations included gains of 1q21.1-31.1 and 20q11.21-13.33, and losses of 11q22.3-25 and 13q14.3-21.33. Subsequent FISH analysis for hTR, located at 3q26, confirmed the presence of 3q gain in SCCs and HPV-immortalized cell lines. Fine mapping of chromosome 20q using multiplex ligation-dependent probe amplification (MLPA) showed copy number increases for a number of genes located at 20q11-q12, including DNMT3B and TOP1. For DNMT3B, this correlated with elevated mRNA expression in 79\% of cases. In conclusion, the assessment of frequent genomic alterations resulted in the identification of potential novel biomarkers, which may ultimately enable a better risk stratification of high-risk (hr)-HPV-positive women.

}, keywords = {Adenocarcinoma, Adult, Aged, Carcinoma, Squamous Cell, Cell Line, Tumor, Chromosome Aberrations, Chromosome Mapping, Chromosomes, Human, Chromosomes, Human, Pair 20, DNA (Cytosine-5-)-Methyltransferase, Female, Genome, Human, Humans, In Situ Hybridization, Fluorescence, Middle Aged, Oligonucleotide Array Sequence Analysis, Papillomaviridae, RNA, Messenger, RNA, Neoplasm, Uterine Cervical Neoplasms}, issn = {0022-3417}, doi = {10.1002/path.1966}, author = {Wilting, S M and Snijders, P J F and Meijer, G A and Ylstra, B and van den Ijssel, P R L A and A Snijders and Albertson, D G and Coffa, J and Schouten, J P and van de Wiel, M A and Meijer, C J L M and Steenbergen, R D M} } @article {267, title = {The BAC resource: tools for array CGH and FISH.}, journal = {Curr Protoc Hum Genet}, volume = {Chapter 4}, year = {2005}, month = {2005 Aug}, pages = {Unit 4.13}, abstract = {

Bacterial Artificial Chromosome (BAC) vector clones carrying human DNA were chosen as the intermediate templates for the sequencing of the human genome due to their inherent stability and fidelity to the genome sequence from which they were derived. In this unit, we describe a set of protocols for BAC-based array comparative genomic hybridization (aCGH) that comprise the generation of targets for printing solutions onto glass slides, the subsequent hybridization steps, and CGH analysis of a test sample compared to a reference normal sample. The BAC clones through their sequence allow the extent and gene content of numerical aberrations to be delineated by aCGH, and also provide cytogeneticists with tools for subsequent validation or fine mapping studies.

}, keywords = {Chromosomes, Artificial, Bacterial, Genome, Human, Humans, In Situ Hybridization, Fluorescence, Nucleic Acid Hybridization}, issn = {1934-8258}, doi = {10.1002/0471142905.hg0413s46}, author = {Nowak, Norma J and A Snijders and Conroy, Jeffrey M and Albertson, Donna G} } @article {265, title = {Centromeric chromosomal translocations show tissue-specific differences between squamous cell carcinomas and adenocarcinomas.}, journal = {Oncogene}, volume = {24}, year = {2005}, month = {2005 Feb 24}, pages = {1571-9}, abstract = {

Structural chromosomal aberrations are common in epithelial tumors. Here, we compared the location of centromeric breaks associated with whole arm translocations in seven adenocarcinoma cell lines and nine squamous cell carcinoma cell lines using SKY, microarray-based comparative genomic hybridization (array CGH) and fluorescence in situ hybridization (FISH). Whole arm translocations were more frequent in squamous cell carcinomas (112 in nine cell lines and nine in one short-term culture) than in adenocarcinomas (13 in seven cases) and most often resulted in copy number alterations. Array CGH analysis demonstrated that in all squamous cell carcinomas and in most adenocarcinomas, the breakpoints of unbalanced whole arm translocations occurred between the two clones on the array flanking the centromeres. However, FISH with centromeric probes revealed that in squamous cell carcinomas, the marker chromosomes with whole arm translocations contained centromeres comprised of material from both participating chromosomes, while in adenocarcinomas centromeric material from only one of the chromosomes was present. These observations suggest that different mechanisms of centromeric instability underlie the formation of chromosomal aberrations in adenocarcinomas and squamous cell carcinomas.

}, keywords = {Adenocarcinoma, Carcinoma, Squamous Cell, Cell Line, Tumor, Centromere, Chromosome Mapping, Chromosomes, Human, Diagnosis, Differential, Humans, In Situ Hybridization, Fluorescence, Karyotyping, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Translocation, Genetic}, issn = {0950-9232}, doi = {10.1038/sj.onc.1208294}, author = {Hermsen, Mario and A Snijders and Guerv{\'o}s, Marta Alonso and Taenzer, Simone and Koerner, Ulrike and Baak, Jan and Pinkel, Daniel and Albertson, Donna and van Diest, Paul and Meijer, Gerrit and Schrock, Evelin} } @article {264, title = {High-resolution mapping of genotype-phenotype relationships in cri du chat syndrome using array comparative genomic hybridization.}, journal = {Am J Hum Genet}, volume = {76}, year = {2005}, month = {2005 Feb}, pages = {312-26}, abstract = {

We have used array comparative genomic hybridization to map DNA copy-number changes in 94 patients with cri du chat syndrome who had been carefully evaluated for the presence of the characteristic cry, speech delay, facial dysmorphology, and level of mental retardation (MR). Most subjects had simple deletions involving 5p (67 terminal and 12 interstitial). Genotype-phenotype correlations localized the region associated with the cry to 1.5 Mb in distal 5p15.31, between bacterial artificial chromosomes (BACs) containing markers D5S2054 and D5S676; speech delay to 3.2 Mb in 5p15.32-15.33, between BACs containing D5S417 and D5S635; and the region associated with facial dysmorphology to 2.4 Mb in 5p15.2-15.31, between BACs containing D5S208 and D5S2887. These results overlap and refine those reported in previous publications. MR depended approximately on the 5p deletion size and location, but there were many cases in which the retardation was disproportionately severe, given the 5p deletion. All 15 of these cases, approximately two-thirds of the severely retarded patients, were found to have copy-number aberrations in addition to the 5p deletion. Restriction of consideration to patients with only 5p deletions clarified the effect of such deletions and suggested the presence of three regions, MRI-III, with differing effect on retardation. Deletions including MRI, a 1.2-Mb region overlapping the previously defined cri du chat critical region but not including MRII and MRIII, produced a moderate level of retardation. Deletions restricted to MRII, located just proximal to MRI, produced a milder level of retardation, whereas deletions restricted to the still-more proximal MRIII produced no discernible phenotype. However, MR increased as deletions that included MRI extended progressively into MRII and MRIII, and MR became profound when all three regions were deleted.

}, keywords = {Adult, Child, Chromosome Mapping, Chromosomes, Human, Pair 5, Cri-du-Chat Syndrome, DNA Mutational Analysis, Genotype, Humans, Intellectual Disability, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Phenotype, Severity of Illness Index}, issn = {0002-9297}, doi = {10.1086/427762}, author = {Zhang, Xiaoxiao and A Snijders and Segraves, Richard and Zhang, Xiuqing and Niebuhr, Anita and Albertson, Donna and Yang, Huanming and Gray, Joe and Niebuhr, Erik and Bolund, Lars and Pinkel, Dan} } @article {147, title = {Mapping segmental and sequence variations among laboratory mice using BAC array CGH.}, journal = {Genome Res}, volume = {15}, year = {2005}, month = {2005 Feb}, pages = {302-11}, abstract = {

We used arrays of 2069 BACs (1303 nonredundant autosomal clones) to map sequence variation among Mus spretus (SPRET/Ei and SPRET/Glasgow) and Mus musculus (C3H/HeJ, BALB/cJ, 129/J, DBA/2J, NIH, FVB/N, and C57BL/6) strains. We identified 80 clones representing 74 autosomal loci of copy number variation (|log(2)ratio| >/= 0.4). These variant loci distinguish laboratory strains. By FISH mapping, we determined that 63 BACs mapped to a single site on C57BL/6J chromosomes, while 17 clones mapped to multiple chromosomes (n = 16) or multiple sites on one chromosome (n = 1). We also show that small ratio changes (Delta log(2)ratio approximately 0.1) distinguish homozygous and heterozygous regions of the genome in interspecific backcross mice, providing an efficient method for genotyping progeny of backcrosses.

}, keywords = {Animals, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Crosses, Genetic, Gene Dosage, Genetic Markers, Genetic Variation, Genome, Mice, Mice, Inbred BALB C, Mice, Inbred C3H, Mice, Inbred C57BL, Mice, Inbred DBA, Mice, Inbred Strains, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Species Specificity}, issn = {1088-9051}, doi = {10.1101/gr.2902505}, author = {A Snijders and Nowak, Norma J and Huey, Bing and Fridlyand, Jane and Law, Sindy and Conroy, Jeffrey and Tokuyasu, Taku and Demir, Kubilay and Chiu, Readman and Jiang-Hua Mao and Jain, Ajay N and Jones, Steven J M and Balmain, Allan and Pinkel, Daniel and Albertson, Donna G} } @article {266, title = {Rare amplicons implicate frequent deregulation of cell fate specification pathways in oral squamous cell carcinoma.}, journal = {Oncogene}, volume = {24}, year = {2005}, month = {2005 Jun 16}, pages = {4232-42}, abstract = {

Genomes of solid tumors are characterized by gains and losses of regions, which may contribute to tumorigenesis by altering gene expression. Often the aberrations are extensive, encompassing whole chromosome arms, which makes identification of candidate genes in these regions difficult. Here, we focused on narrow regions of gene amplification to facilitate identification of genetic pathways important in oral squamous cell carcinoma (SCC) development. We used array comparative genomic hybridization (array CGH) to define minimum common amplified regions and then used expression analysis to identify candidate driver genes in amplicons that spanned \<3 Mb. We found genes involved in integrin signaling (TLN1), survival (YAP1, BIRC2), and adhesion and migration (TLN1, LAMA3, MMP7), as well as members of the hedgehog (GLI2) and notch (JAG1, RBPSUH, FJX1) pathways to be amplified and overexpressed. Deregulation of these and other members of the hedgehog and notch pathways (HHIP, SMO, DLL1, NOTCH4) implicates deregulation of developmental and differentiation pathways, cell fate misspecification, in oral SCC development.

}, keywords = {Carcinoma, Squamous Cell, Cell Adhesion, Cell Survival, Cell Transformation, Neoplastic, Gene Amplification, Gene Expression Regulation, Neoplastic, Humans, Mouth Neoplasms, Oligonucleotide Array Sequence Analysis, Signal Transduction}, issn = {0950-9232}, doi = {10.1038/sj.onc.1208601}, author = {A Snijders and Schmidt, Brian L and Fridlyand, Jane and Dekker, Nusi and Pinkel, Daniel and Jordan, Richard C K and Albertson, Donna G} } @article {262, title = {BAC microarray-based comparative genomic hybridization.}, journal = {Methods Mol Biol}, volume = {256}, year = {2004}, month = {2004}, pages = {39-56}, keywords = {Base Sequence, Chromosomes, Artificial, Bacterial, DNA Primers, DNA Restriction Enzymes, Genomics, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction}, issn = {1064-3745}, doi = {10.1385/1-59259-753-X:039}, author = {A Snijders and Segraves, Richard and Blackwood, Stephanie and Pinkel, Daniel and Albertson, Donna G} } @article {261, title = {Genomic alterations in primary gastric adenocarcinomas correlate with clinicopathological characteristics and survival.}, journal = {Cell Oncol}, volume = {26}, year = {2004}, month = {2004}, pages = {307-17}, abstract = {

BACKGROUND \& AIMS: Pathogenesis of gastric cancer is driven by an accumulation of genetic changes that to a large extent occur at the chromosomal level. In order to investigate the patterns of chromosomal aberrations in gastric carcinomas, we performed genome-wide microarray based comparative genomic hybridisation (microarray CGH). With this recently developed technique chromosomal aberrations can be studied with high resolution and sensitivity.

METHODS: Array CGH was applied to a series of 35 gastric adenocarcinomas using a genome-wide scanning array with 2275 BAC and P1 clones spotted in triplicate. Each clone contains at least one STS for linkage to the sequence of the human genome. These arrays provide an average resolution of 1.4 Mb across the genome. DNA copy number changes were correlated with clinicopathological tumour characteristics as well as survival.

RESULTS: All thirty-five cancers showed chromosomal aberrations and 16 of the 35 tumours showed one or more amplifications. The most frequent aberrations are gains of 8q24.2, 8q24.1, 20q13.12, 20q13.2, 7p11.2, 1q32.3, 8p23.1-p23.3, losses of 5q14.1, 18q22.1, 19p13.12-p13.3, 9p21.3-p24.3, 17p13.1-p13.3, 13q31.1, 16q22.1, 21q21.3, and amplifications of 7q21-q22, and 12q14.1-q21.1. These aberrations were correlated to clinicopathological characteristics and survival. Gain of 1q32.3 was significantly correlated with lymph node status (p=0.007). Tumours with loss of 18q22.1, as well as tumours with amplifications were associated with poor survival (p=0.02, both).

CONCLUSIONS: Microarray CGH has revealed several chromosomal regions that have not been described before in gastric cancer at this frequency and resolution, such as amplification of at 7q21-q22 and 12q14.1-q21.1, as well gains at 1q32.3, 7p11.2, and losses at 13q13.1. Interestingly, gain of 1q32.3 and loss of 18q22.1 are associated with a bad prognosis indicating that these regions could harbour gene(s) that may determine aggressive tumour behaviour and poor clinical outcome.

}, keywords = {Adenocarcinoma, Adult, Aged, Aged, 80 and over, Chromosome Aberrations, Chromosomes, Female, Gene Expression Regulation, Neoplastic, Genetic Linkage, Genome, Human, Humans, Image Processing, Computer-Assisted, Lymph Nodes, Lymphatic Metastasis, Male, Middle Aged, Models, Genetic, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Sensitivity and Specificity, Sequence Tagged Sites, Stomach Neoplasms, Time Factors}, issn = {1570-5870}, author = {Weiss, Marjan M and Kuipers, Ernst J and Postma, Cindy and A Snijders and Pinkel, Daniel and Meuwissen, Stefan G M and Albertson, Donna and Meijer, Gerrit A} } @article {263, title = {A tiling resolution DNA microarray with complete coverage of the human genome.}, journal = {Nat Genet}, volume = {36}, year = {2004}, month = {2004 Mar}, pages = {299-303}, abstract = {

We constructed a tiling resolution array consisting of 32,433 overlapping BAC clones covering the entire human genome. This increases our ability to identify genetic alterations and their boundaries throughout the genome in a single comparative genomic hybridization (CGH) experiment. At this tiling resolution, we identified minute DNA alterations not previously reported. These alterations include microamplifications and deletions containing oncogenes, tumor-suppressor genes and new genes that may be associated with multiple tumor types. Our findings show the need to move beyond conventional marker-based genome comparison approaches, that rely on inference of continuity between interval markers. Our submegabase resolution tiling set for array CGH (SMRT array) allows comprehensive assessment of genomic integrity and thereby the identification of new genes associated with disease.

}, keywords = {Chromosomes, Artificial, Bacterial, Gene Dosage, Genome, Human, Humans, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Sensitivity and Specificity, Tumor Cells, Cultured}, issn = {1061-4036}, doi = {10.1038/ng1307}, author = {Ishkanian, Adrian S and Malloff, Chad A and Watson, Spencer K and DeLeeuw, Ronald J and Chi, Bryan and Coe, Bradley P and A Snijders and Albertson, Donna G and Pinkel, Daniel and Marra, Marco A and Ling, Victor and MacAulay, Calum and Lam, Wan L} } @article {256, title = {Current status and future prospects of array-based comparative genomic hybridisation.}, journal = {Brief Funct Genomic Proteomic}, volume = {2}, year = {2003}, month = {2003 Apr}, pages = {37-45}, abstract = {

The majority of human cancers as well as many developmental abnormalities harbour chromosomal imbalances, many of which result in the gain and/or loss of genomic material. Conventional comparative genomic hybridisation (CGH) has been used extensively to map DNA copy number changes to chromosomal positions. The introduction of microarray CGH provided a powerful tool to precisely detect and quantify genomic aberrations and map these directly onto the sequence of the human genome. In the past several years, a number of different approaches towards array-based CGH have been undertaken. This paper reviews these approaches and presents some of the recently-developed applications of this new technology in both research and clinical settings.

}, keywords = {Chromosome Aberrations, DNA, Neoplasm, Gene Dosage, Genetic Markers, Humans, In Situ Hybridization, Fluorescence, Neoplasms, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis}, issn = {1473-9550}, author = {A Snijders and Pinkel, Daniel and Albertson, Donna G} } @article {257, title = {Determination of amplicon boundaries at 20q13.2 in tissue samples of human gastric adenocarcinomas by high-resolution microarray comparative genomic hybridization.}, journal = {J Pathol}, volume = {200}, year = {2003}, month = {2003 Jul}, pages = {320-6}, abstract = {

Comparative genomic hybridization (CGH) of gastric adenocarcinomas frequently shows gains and amplifications of chromosome 20. However, the underlying genetic lesion is unknown and conventional CGH results do not allow specification of the target region. In order to investigate this chromosomal aberration with a higher resolution and sensitivity, microarray-based CGH was performed with both scanning and high-resolution arrays of chromosome 20 in a series of 27 gastric adenocarcinomas. Locus-specific fragments of genomic DNA from bacterial artificial chromosome (BAC) clones were spotted as microarrays. A scanning array contained a set of 27 BAC clones covering chromosome 20q. A high-resolution array contained 27 overlapping BAC clones at 20q13.2. This high-resolution array was used to narrow down the amplicon at 20q13.2 in tumours showing amplification of this chromosomal region with the scanning array. Positive copy number changes on chromosome 20q were detected in 12 of 27 cases (44\%). These changes included gain of the whole arm of chromosome 20q in 8 of 27 (30\%) cases, amplification restricted to 20q12.1 in one case, and amplifications restricted to 20q13 in three cases (11\%). The three tumours showing amplification restricted to 20q13 were analysed further using the high-resolution array. In one tumour, the whole contig was amplified at a constant level. One of the other two tumours had a clear proximal breakpoint, while the other tumour had a clear distal breakpoint within the 20q13.2 region. The proximal and the distal breakpoint were approximately 800 kb apart. In the present study, an amplicon at 20q13.2 has been narrowed down to 800 kb which is likely to harbour one or more putative oncogenes relevant to gastric carcinogenesis, for which ZNF217 and CYP24 are good candidates.

}, keywords = {Adenocarcinoma, Adult, Aged, Aged, 80 and over, Chromosome Aberrations, Chromosomes, Artificial, Bacterial, Chromosomes, Human, Pair 20, DNA, Neoplasm, Female, Gene Amplification, Humans, In Situ Hybridization, Fluorescence, Male, Middle Aged, Oligonucleotide Array Sequence Analysis, Stomach Neoplasms}, issn = {0022-3417}, doi = {10.1002/path.1359}, author = {Weiss, Marjan M and A Snijders and Kuipers, Ernst J and Ylstra, Bauke and Pinkel, Daniel and Meuwissen, Stefan G M and van Diest, Paul J and Albertson, Donna G and Meijer, Gerrit A} } @article {260, title = {Genome wide array comparative genomic hybridisation analysis of premalignant lesions of the stomach.}, journal = {Mol Pathol}, volume = {56}, year = {2003}, month = {2003 Oct}, pages = {293-8}, abstract = {

BACKGROUND: Gastric cancer is one of the most frequent malignancies in the world, ranking fifth in the Netherlands as a cause of cancer death. Surgery is the only curative treatment for advanced cases, but results of gastrectomy largely depend on the stage of the disease. A better understanding of the mechanisms of progression from a preneoplastic condition through intraepithelial neoplasia to invasive cancer may provide information relevant to designing focused prevention strategies.

METHODS: Because the pattern of chromosomal aberrations in precursors of gastric cancer is unclear, 11 gastric polyps with intraepithelial neoplasia (three hyperplastic polyps and eight adenomas) were analysed by microarray comparative genomic hybridisation to study chromosomal instability in precursors of gastric cancer.

RESULTS: Chromosomal aberrations were detected in all specimens. Adenomas showed no more chromosomal aberrations than did the hyperplastic polyps. The most frequent aberrations were gain of 7q36 and 20q12, and loss of 5q14-q21 in the adenomas, and loss of 15q11-14, 1p21-31, and 21q11-21.2 in the hyperplastic polyps. The most frequent chromosomal aberration in common to both types was loss of 9p21.3.

CONCLUSION: Hyperplastic polyps showed many chromosomal aberrations, confirming that neoplastic transformation can occur in these lesions. These observations are consistent with the existence of two morphologically and genetically distinct pathways to gastric cancer-the hyperplastic polyp pathway and the (intestinal type) adenoma pathway. The relative contribution of each to gastric carcinogenesis in general, and how they compare to patterns of chromosomal aberrations in the more prevalent flat foci of intraepithelial neoplasia remain to be determined.

}, keywords = {Adenoma, Carcinoma in Situ, Chromosome Aberrations, Disease Progression, Female, Genome, Humans, Hyperplasia, Male, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Precancerous Conditions, Stomach, Stomach Neoplasms}, issn = {1366-8714}, author = {Weiss, M M and Kuipers, E J and Postma, C and A Snijders and Stolte, M and Vieth, M and Pinkel, D and Meuwissen, S G M and Albertson, D and Meijer, G A} } @article {258, title = {Genome-wide-array-based comparative genomic hybridization reveals genetic homogeneity and frequent copy number increases encompassing CCNE1 in fallopian tube carcinoma.}, journal = {Oncogene}, volume = {22}, year = {2003}, month = {2003 Jul 3}, pages = {4281-6}, abstract = {

Fallopian tube carcinoma (FTC) is a rare, poorly studied and aggressive cancer, associated with poor survival. Since tumorigenesis is related to the acquisition of genetic changes, we used genome-wide array comparative genomic hybridization to analyse copy number aberrations occurring in FTC in order to obtain a better understanding of FTC carcinogenesis and to identify prognostic events and targets for therapy. We used arrays of 2464 genomic clones, providing approximately 1.4 Mb resolution across the genome to map genomic DNA copy number aberrations quantitatively from 14 FTC onto the human genome sequence. All tumors showed a high frequency of copy number aberrations with recurrent gains on 3q, 6p, 7q, 8q, 12p, 17q, 19 and 20q, and losses involving chromosomes 4, 5q, 8p, 16q, 17p, 18q and X. Recurrent regions of amplification included 1p34, 8p11-q11, 8q24, 12p, 17p13, 17q12-q21, 19p13, 19q12-q13 and 19q13. Candidate, known oncogenes mapping to these amplicons included CMYC (8q24), CCNE1 (19q12-q21) and AKT2 (19q13), whereas PIK3CA and KRAS, previously suggested to be candidate driver genes for amplification, mapped outside copy number maxima on 3q and 12p, respectively. The FTC were remarkably homogeneous, with some recurrent aberrations occurring in more than 70\% of samples, which suggests a stereotyped pattern of tumor evolution.

}, keywords = {Carcinoma, Chromosome Mapping, Cyclin E, DNA, Fallopian Tube Neoplasms, Female, Gene Expression Regulation, Neoplastic, Genome, Humans, Models, Genetic, Mutation, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Oncogene Proteins, Oncogenes}, issn = {0950-9232}, doi = {10.1038/sj.onc.1206621}, author = {A Snijders and Nowee, Marlies E and Fridlyand, Jane and Piek, Jurgen M J and Dorsman, Josephine C and Jain, Ajay N and Pinkel, Daniel and van Diest, Paul J and Verheijen, Ren{\'e} H M and Albertson, Donna G} } @article {255, title = {Genomic profiling of gastric cancer predicts lymph node status and survival.}, journal = {Oncogene}, volume = {22}, year = {2003}, month = {2003 Mar 27}, pages = {1872-9}, abstract = {

Gastric carcinogenesis is driven by an accumulation of genetic changes that to a large extent occur at the chromosomal level. We analysed the patterns of chromosomal instability in 35 gastric carcinomas and their clinical correlations. With microarray competitive genomic hybridization, genomewide chromosomal copy number changes can be studied with high resolution and sensitivity. A genomewide scanning array with 2275 BAC and P1 clones spotted in triplicate was used. This array provided an average resolution of 1.4 Mb across the genome. Patterns of chromosomal aberrations were analysed by hierarchical cluster analysis of the normalized log(2) tumour to normal fluorescence ratios of all clones, and cluster membership was correlated to clinicopathological data including survival. Hierarchical cluster analysis revealed three groups with different genomic profiles that correlated significantly with lymph node status (P=0.02). Moreover, gastric cancer cases from cluster 3 showed a significantly better prognosis than those from clusters 1 and 2 (P=0.02). Genomic profiling of gastric adenocarcinomas based on microarray analysis of chromosomal copy number changes predicted lymph node status and survival. The possibility to discriminate between patients with a high risk of lymph node metastasis could clinically be helpful for selecting patients for extended lymph node resection.

}, keywords = {Animals, Lymphatic Metastasis, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Prognosis, Stomach Neoplasms, Survival Analysis}, issn = {0950-9232}, doi = {10.1038/sj.onc.1206350}, author = {Weiss, Marjan M and Kuipers, Ernst J and Postma, Cindy and A Snijders and Siccama, Ivar and Pinkel, Daniel and Westerga, Johan and Meuwissen, Stefan G M and Albertson, Donna G and Meijer, Gerrit A} } @article {259, title = {Shaping of tumor and drug-resistant genomes by instability and selection.}, journal = {Oncogene}, volume = {22}, year = {2003}, month = {2003 Jul 10}, pages = {4370-9}, abstract = {

Tumors with defects in mismatch repair (MMR) show fewer chromosomal changes by cytogenetic analyses than most solid tumors, suggesting that a greater proportion of the alterations required for malignancy occur in genes with nucleotide sequences susceptible to errors normally corrected by MMR. Here, we used genome-wide microarray comparative genomic hybridization to carry out a higher resolution evaluation of the effect of MMR competence on genomic alterations occurring in 20 cell lines and to determine if characteristic aberrations arise in MMR-proficient and -deficient HCT116 cells undergoing selection for methotrexate resistance. We observed different spectra of aberrations in MMR-proficient compared to -deficient cell lines, as well as among cell lines with different types of MMR-deficiency. We also observed different genetic routes to drug resistance. Resistant MMR-deficient cells most frequently displayed no copy number alterations (16/29 cell pools), whereas all MMR-proficient cells had unique abnormalities involving chromosome 5, including amplicons centered on the target gene, DHFR and/or a neighboring novel locus (7/13 pools). These observations support the concept that tumor genomes are shaped by selection for alterations that promote survival and growth advantage, as well as by the particular dysfunctions in genes responsible for maintenance of genetic integrity.

}, keywords = {Base Pair Mismatch, Cell Line, DNA Repair, Drug Resistance, Neoplasm, Gene Dosage, Genome, Humans, Methotrexate, Neoplasms, Tetrahydrofolate Dehydrogenase}, issn = {0950-9232}, doi = {10.1038/sj.onc.1206482}, author = {A Snijders and Fridlyand, Jane and Mans, Dorus A and Segraves, Richard and Jain, Ajay N and Pinkel, Daniel and Albertson, Donna G} } @article {254, title = {Fully automatic quantification of microarray image data.}, journal = {Genome Res}, volume = {12}, year = {2002}, month = {2002 Feb}, pages = {325-32}, abstract = {

DNA microarrays are now widely used to measure expression levels and DNA copy number in biological samples. Ratios of relative abundance of nucleic acids are derived from images of regular arrays of spots containing target genetic material to which fluorescently labeled samples are hybridized. Whereas there are a number of methods in use for the quantification of images, many of the software systems in wide use either encourage or require extensive human interaction at the level of individual spots on arrays. We present a fully automatic system for microarray image quantification. The system automatically locates both subarray grids and individual spots, requiring no user identification of any image coordinates. Ratios are computed based on explicit segmentation of each spot. On a typical image of 6000 spots, the entire process takes less than 20 sec. We present a quantitative assessment of performance on multiple replicates of genome-wide array-based comparative genomic hybridization experiments. By explicitly identifying the pixels in each spot, the system yields more accurate estimates of ratios than systems assuming spot circularity. The software, called, runs on Windows platforms and is available free of charge for academic use.

}, keywords = {Breast Neoplasms, Female, Gene Expression Profiling, Humans, Image Processing, Computer-Assisted, Male, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis, Staining and Labeling, Tumor Cells, Cultured}, issn = {1088-9051}, doi = {10.1101/gr.210902}, author = {Jain, Ajay N and Tokuyasu, Taku A and A Snijders and Segraves, Richard and Albertson, Donna G and Pinkel, Daniel} } @article {253, title = {Assembly of microarrays for genome-wide measurement of DNA copy number.}, journal = {Nat Genet}, volume = {29}, year = {2001}, month = {2001 Nov}, pages = {263-4}, abstract = {

We have assembled arrays of approximately 2,400 BAC clones for measurement of DNA copy number across the human genome. The arrays provide precise measurement (s.d. of log2 ratios=0.05-0.10) in cell lines and clinical material, so that we can reliably detect and quantify high-level amplifications and single-copy alterations in diploid, polyploid and heterogeneous backgrounds.

}, keywords = {Aneuploidy, Chromosomes, Artificial, Bacterial, Cloning, Molecular, Female, Gene Dosage, Genome, Human, Genomics, Humans, Male, Oligonucleotide Array Sequence Analysis, Polymerase Chain Reaction, Polyploidy, Tumor Cells, Cultured, X Chromosome}, issn = {1061-4036}, doi = {10.1038/ng754}, author = {A Snijders and Nowak, N and Segraves, R and Blackwood, S and Brown, N and Conroy, J and Hamilton, G and Hindle, A K and Huey, B and Kimura, K and Law, S and Myambo, K and Palmer, J and Ylstra, B and Yue, J P and Gray, J W and Jain, A N and Pinkel, D and Albertson, D G} } @article {252, title = {Comparative genomic hybridization of microdissected familial ovarian carcinoma: two deleted regions on chromosome 15q not previously identified in sporadic ovarian carcinoma.}, journal = {Lab Invest}, volume = {81}, year = {2001}, month = {2001 Oct}, pages = {1363-70}, abstract = {

The vast majority of familial ovarian cancers harbor a germline mutation in either the breast cancer gene BRCA1 or BRCA2 tumor suppressor genes. However, mutations of these genes in sporadic ovarian cancer are rare. This suggests that in contrast to hereditary disease, BRCA1 and BRCA2 are not commonly involved in sporadic ovarian cancer and may indicate that there are two distinct pathways for the development of ovarian cancer. To characterize further differences between hereditary and sporadic cancers, the comparative genomic hybridization technique was employed to analyze changes in copy number of genetic material in a panel of 36 microdissected hereditary ovarian cancers. Gains at 8q23-qter (18 of 36, 5 cases with high-level amplifications), 3q26.3-qter (18 of 36, 2 cases with high-level amplifications), 11q22 (11 of 36) and 2q31-32 (8 of 36) were most frequent. Losses most frequently occurred (in decreasing order of frequency) on 8p21-pter (23 of 36), 16q22-pter (19 of 36), 22q13 (19 of 36), 9q31-33 (16 of 36), 12q24 (16 of 36), 15q11-15 (16 of 36), 17p12-13 (14 of 36), Xp21-22 (14 of 36), 20q13 (13 of 36), 15q24-25 (12 of 36), and 18q21 (12 of 36). Comparison with the literature revealed that the majority of these genetic alterations are also common in sporadic ovarian cancer. Deletions of 15q11-15, 15q24-25, 8p21-ter, 22q13, 12q24 and gains at 11q22, 13q22, and 17q23-25, however, appear to be specific to hereditary ovarian cancer. Aberrations at 15q11-15 and 15q24-25 have not yet been described in familial ovarian cancer. In these regions, important tumor suppressor genes, including the hRAD51 gene, are located. These and other yet unknown suppressor genes may be involved in a specific carcinogenic pathway for familial ovarian cancer and may explain the distinct clinical presentation and behavior of familial ovarian cancer.

}, keywords = {BRCA2 Protein, Chromosomes, Human, Pair 15, Female, Genes, BRCA1, Genetic Markers, Humans, Nucleic Acid Hybridization, Ovarian Neoplasms, Sequence Deletion}, issn = {0023-6837}, author = {Zweemer, R P and Ryan, A and A Snijders and Hermsen, M A and Meijer, G A and Beller, U and Menko, F H and Jacobs, I J and Baak, J P and Verheijen, R H and Kenemans, P and van Diest, P J} } @article {251, title = {Integration of cytogenetic landmarks into the draft sequence of the human genome.}, journal = {Nature}, volume = {409}, year = {2001}, month = {2001 Feb 15}, pages = {953-8}, abstract = {

We have placed 7,600 cytogenetically defined landmarks on the draft sequence of the human genome to help with the characterization of genes altered by gross chromosomal aberrations that cause human disease. The landmarks are large-insert clones mapped to chromosome bands by fluorescence in situ hybridization. Each clone contains a sequence tag that is positioned on the genomic sequence. This genome-wide set of sequence-anchored clones allows structural and functional analyses of the genome. This resource represents the first comprehensive integration of cytogenetic, radiation hybrid, linkage and sequence maps of the human genome; provides an independent validation of the sequence map and framework for contig order and orientation; surveys the genome for large-scale duplications, which are likely to require special attention during sequence assembly; and allows a stringent assessment of sequence differences between the dark and light bands of chromosomes. It also provides insight into large-scale chromatin structure and the evolution of chromosomes and gene families and will accelerate our understanding of the molecular bases of human disease and cancer.

}, keywords = {Chromosome Aberrations, Chromosome Mapping, Chromosomes, Artificial, Bacterial, Cytogenetic Analysis, Genetic Markers, Genome, Human, Human Genome Project, Humans, In Situ Hybridization, Fluorescence, Radiation Hybrid Mapping, Sequence Tagged Sites}, issn = {0028-0836}, doi = {10.1038/35057192}, author = {Cheung, V G and Nowak, N and Jang, W and Kirsch, I R and Zhao, S and Chen, X N and Furey, T S and Kim, U J and Kuo, W L and Olivier, M and Conroy, J and Kasprzyk, A and Massa, H and Yonescu, R and Sait, S and Thoreen, C and A Snijders and Lemyre, E and Bailey, J A and Bruzel, A and Burrill, W D and Clegg, S M and Collins, S and Dhami, P and Friedman, C and Han, C S and Herrick, S and Lee, J and Ligon, A H and Lowry, S and Morley, M and Narasimhan, S and Osoegawa, K and Peng, Z and Plajzer-Frick, I and Quade, B J and Scott, D and Sirotkin, K and Thorpe, A A and Gray, J W and Hudson, J and Pinkel, D and Ried, T and Rowen, L and Shen-Ong, G L and Strausberg, R L and Birney, E and Callen, D F and Cheng, J F and Cox, D R and Doggett, N A and Carter, N P and Eichler, E E and Haussler, D and Korenberg, J R and Morton, C C and Albertson, D and Schuler, G and de Jong, P J and Trask, B J} } @article {250, title = {Microarray techniques in pathology: tool or toy?}, journal = {Mol Pathol}, volume = {53}, year = {2000}, month = {2000 Dec}, pages = {289-94}, abstract = {

Microarray technology allows the simultaneous analysis of up to thousands of different genes in histological or cytological specimens. Although microarray technology has so far mainly been applied in the research setting, its clinical application in pathology is expected in the foreseeable future. This paper presents an overview of the technical "ins and outs" of microarray technology, and discusses several putative applications in diagnostic pathology, which include tumour classification, the prediction of responses to certain chemotherapeutical or hormonal agents, the biological staging of tumours, the risk assessment of premalignant lesions, and the detection of microorganisms.

}, keywords = {DNA Mutational Analysis, Gene Expression Profiling, Humans, Neoplasms, Nucleic Acid Hybridization, Oligonucleotide Array Sequence Analysis}, issn = {1366-8714}, author = {A Snijders and Meijer, G A and Brakenhoff, R H and van den Brule, A J and van Diest, P J} } @article {249, title = {CD40 engagement modulates the production of matrix metalloproteinases by gingival fibroblasts.}, journal = {Clin Exp Immunol}, volume = {115}, year = {1999}, month = {1999 Jan}, pages = {161-7}, abstract = {

Chronic periodontitis is a destructive inflammatory disease linked with unbalanced production between matrix metalloproteinases (MMPs), such as interstitial collagenase (MMP-1) and stromelysin-1 (MMP-3) and their endogenous tissue inhibitors of MMPs (TIMPs). In addition to aberrant MMP-1 and MMP-3 expression, periodontal lesions are characterized by dense infiltrations of activated T lymphocytes which may interact with CD40-expressing gingival fibroblasts in the connective tissue via the CD40L-CD40 pathway. In this study we investigated whether CD40 cross-linking influenced MMP production by gingival fibroblasts. Therefore, we analysed the CD40L-induced MMP production by these fibroblasts in the presence of cytokines that are increased in periodontal lesions, such as IL-1beta, tumour necrosis factor-alpha (TNF-alpha) and interferon-gamma (IFN-gamma). We show that CD40 ligation on gingival fibroblasts resulted in a decrease of their MMP-1 and MMP-3 production, while MMP-2 and TIMP-1 production were unaffected as determined by Western blot. This down-regulatory effect of CD40 engagement on MMP-1 and MMP-3 production by gingival fibroblasts was also present when MMP production was up-regulated by IL-1beta and TNF-alpha or down-regulated by IFN-gamma. These results suggest that CD40 ligation on gingival fibroblasts leads to a restraining of MMP-1 and MMP-3 production by gingival fibroblasts and thereby may be an important mechanism in the retardation of further periodontal tissue damage.

}, keywords = {Adult, Antigens, CD40, Extracellular Matrix, Fibroblasts, Gingiva, Humans, Interferon-gamma, Interleukin-1, Interleukin-6, Interleukin-8, Metalloendopeptidases, Tumor Necrosis Factor-alpha}, issn = {0009-9104}, author = {Wassenaar, A and Verschoor, T and Kievits, F and Den Hartog, M T and Kapsenberg, M L and Everts, V and A Snijders} } @article {247, title = {Characteristics of Prevotella intermedia-specific CD4+ T cell clones from peripheral blood of a chronic adult periodontitis patient.}, journal = {Clin Exp Immunol}, volume = {113}, year = {1998}, month = {1998 Jul}, pages = {105-10}, abstract = {

Periodontitis is a chronic destructive inflammatory disease associated with periodontopathic bacteria. In addition, autoantigens such as collagen and heat shock proteins (hsp) have been suggested to play a role. Established periodontal lesions are characterized by dense infiltrations of immune cells such as cytokine-producing CD4+ and CD8+ T cells. CD4+ T cells specific for Prevotella intermedia can be isolated from lesional gingiva, suggesting an active role for CD4+ T cells in the response to this bacterium. We therefore investigated the characteristics of a panel of 13 P. intermedia-specific CD4+ T cells generated from the peripheral blood of a patient with chronic adult periodontitis. All 13 P. intermedia-specific CD4+ T cells recognized the antigens in the context of HLA-DR. The T cell clones were mainly classified as Th0, producing comparable amounts of interferon-gamma (IFN-gamma) and IL-4, and Th2, producing high amounts of IL-4 and almost no IFN-gamma. None of the P. intermedia-specific T cell clones recognized antigens of the periodontopathic bacteria Actinobacillus actinomycetemcomitans and Porphyromonas gingivalis and of the autoantigens collagen and hsp. The reactivity profile of the T cell clones to size-fractionated cell envelope antigens of P. intermedia indicated that P. intermedia-specific CD4+ T cell clones recognize probably five different antigen specificities in the context of the MHC class II molecules, DR7 or DR15. These results suggest that a broad panel of cell-associated protein antigens play a role in the induction of P. intermedia-specific CD4+ T cell response.

}, keywords = {Adult, Bacteroidaceae Infections, CD4-Positive T-Lymphocytes, Cells, Cultured, Chronic Disease, Clone Cells, HLA-DR Antigens, HLA-DR Serological Subtypes, HLA-DR7 Antigen, Humans, Periodontitis, Prevotella intermedia}, issn = {0009-9104}, author = {Wassenaar, A and Reinhardus, C and Abraham-Inpijn, L and A Snijders and Kievits, F} } @article {246, title = {Enhanced prostaglandin E2 production by monocytes in atopic dermatitis (AD) is not accompanied by enhanced production of IL-6, IL-10 or IL-12.}, journal = {Clin Exp Immunol}, volume = {111}, year = {1998}, month = {1998 Mar}, pages = {472-6}, abstract = {

AD is associated with a bias of the T helper cells to show increased IL-4 and reduced interferon-gamma (IFN-gamma) production. The production of IFN-gamma and IL-4 and the development of Th cells into either high IFN-gamma or high IL-4 producers is strongly influenced by factors produced by antigen-presenting cells (APC), like IL-12 and prostaglandin E2 (PGE2). IL-12 selectively enhances IFN-gamma production and favours the development of IFN-gamma-producing Th cells, whereas PGE2 selectively inhibits IFN-gamma production by Th cells. The aim of this study was to test whether the increased IL-4/IFN-gamma production ratio by Th cells in AD can be explained by an increased PGE2/IL-12 production ratio by the APC. Monocytes were used as APC source. PGE2 and IL-12 production by lipopolysaccharide (LPS)-stimulated monocytes from 12 AD patients and 12 non-atopic controls was determined using two complementary experimental systems, whole blood cultures and purified monocytes. In addition, we determined IL-6 production as a measure of monocyte activation, and IL-10 production because IL-12 production by monocytes is highly influenced by endogenously produced IL-10. The monocytes from AD patients showed normal production levels of IL-6 and IL-10, a two-fold, but non-significant decrease in IL-12 production, and a significantly (three-fold) higher PGE2 production than those from non-atopic controls. Here we show for the first time that enhanced PGE2 production by monocytes in AD is not accompanied by a general rise in cytokine production. We conclude that AD is indeed associated with an increased PGE2/IL-12 production ratio by monocytes.

}, keywords = {Adolescent, Adult, Cells, Cultured, Dermatitis, Atopic, Dinoprostone, Female, Humans, Interferon-gamma, Interleukin-10, Interleukin-12, Interleukin-6, Interleukins, Leukocytes, Mononuclear, Lipopolysaccharides, Lymphocyte Activation, Male, Middle Aged, Stimulation, Chemical}, issn = {0009-9104}, author = {A Snijders and Van der Pouw Kraan, T C and Engel, M and Wormmeester, J and Widjaja, P and Zonneveld, I M and Bos, J D and Kapsenberg, M L} } @article {248, title = {Histamine inhibits the production of interleukin-12 through interaction with H2 receptors.}, journal = {J Clin Invest}, volume = {102}, year = {1998}, month = {1998 Nov 15}, pages = {1866-73}, abstract = {

IL-12 is essential for T helper 1 (Th1) development and inhibits the induction of Th2 responses. Atopic diseases, which are characterized by Th2 responses, are associated with the overproduction of histamine. Here we present evidence that histamine, at physiological concentrations, strongly inhibits human IL-12 p40 and p70 mRNA and protein production by human monocytes. The use of specific histamine receptor antagonists reveals that this inhibition is mediated via the H2 receptor and induction of intracellular cAMP. The inhibition of IL-12 production is independent of IL-10 and IFN-gamma. The observation that histamine strongly reduces the production of the Th1-inducing cytokine IL-12 implies a positive feedback mechanism for the development of Th2 responses in atopic patients.

}, keywords = {Dinoprostone, Histamine, Histamine Agonists, Histamine Antagonists, Histamine H2 Antagonists, Humans, Imidazoles, Interleukin-12, Interleukins, Monocytes, Ranitidine, Receptors, Histamine H2, RNA, Messenger, Thiourea, Triprolidine}, issn = {0021-9738}, doi = {10.1172/JCI3692}, author = {Van der Pouw Kraan, T C and A Snijders and Boeije, L C and de Groot, E R and Alewijnse, A E and Leurs, R and Aarden, L A} } @article {245, title = {Antigen-presenting properties of gingival fibroblasts in chronic adult periodontitis.}, journal = {Clin Exp Immunol}, volume = {110}, year = {1997}, month = {1997 Nov}, pages = {277-84}, abstract = {

Chronic periodontitis is characterized by dense infiltrations of T lymphocytes in the connective tissue, which consists mainly of gingival fibroblasts. It is becoming increasingly clear that T lymphocytes and gingival fibroblasts are capable of influencing each other. For example, the T cell cytokine interferon-gamma (IFN-gamma) is able to induce MHC class II molecules on the surface of several cell types, including gingival fibroblasts. Histological sections of chronically inflamed gingival tissue showed a great number of CD4+ and CD8+ T cells that produced IFN-gamma, and in addition showed abundant expression of MHC class II molecules on gingival fibroblasts. Therefore, we investigated whether these gingival fibroblasts acquire the capacity to carry out MHC class II-restricted functions such as antigen presentation to local T cells. In this study, we show that IFN-gamma-treated gingival fibroblasts were able to function as antigen-presenting cells (APC) for superantigen-mediated T cell proliferation. However, these fibroblasts failed to present whole-cell antigens of periodontitis-associated bacteria. Moreover, gingival fibroblasts inhibited the presentation of the whole-cell antigens of these bacteria by professional APC. This inhibition could be overcome by the addition of IL-2. These results suggest that gingival fibroblasts play an important role in the local specific immune response in chronic inflammatory periodontal lesions by regulating the response of infiltrating T cells.

}, keywords = {Adult, Antigen Presentation, CD4-Positive T-Lymphocytes, CD8-Positive T-Lymphocytes, Chronic Disease, Fibroblasts, Gingiva, Histocompatibility Antigens Class II, Humans, Interferon-gamma, Periodontitis, Superantigens}, issn = {0009-9104}, author = {Wassenaar, A and A Snijders and Abraham-Inpijn, L and Kapsenberg, M L and Kievits, F} }