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1.  Homology-mediated end-capping as a primary step of sister chromatid fusion in the breakage-fusion-bridge cycles 
Nucleic Acids Research  2013;41(21):9732-9740.
Breakage-fusion-bridge (BFB) cycle is a series of chromosome breaks and duplications that could lead to the increased copy number of a genomic segment (gene amplification). A critical step of BFB cycles leading to gene amplification is a palindromic fusion of sister chromatids following the rupture of a dicentric chromosome during mitosis. It is currently unknown how sister chromatid fusion is produced from a mitotic break. To delineate the process, we took an integrated genomic, cytogenetic and molecular approach for the recurrent MCL1 amplicon at chromosome 1 in human tumor cells. A newly developed next-generation sequencing-based approach identified a cluster of palindromic fusions within the amplicon at ∼50-kb intervals, indicating a series of breaks and fusions by BFB cycles. The physical location of the amplicon (at the end of a broken chromosome) further indicated BFB cycles as underlying processes. Three palindromic fusions were mediated by the homologies between two nearby inverted Alu repeats, whereas the other two fusions exhibited microhomology-mediated events. Such breakpoint sequences indicate that homology-mediated fold-back capping of broken ends followed by DNA replication is an underlying mechanism of sister chromatid fusion. Our results elucidate nucleotide-level events during BFB cycles and end processing for naturally occurring mitotic breaks.
doi:10.1093/nar/gkt762
PMCID: PMC3834830  PMID: 23975201
2.  Reduced expression of autotaxin predicts survival in uveal melanoma 
The British Journal of Ophthalmology  2007;91(10):1385-1392.
Aim
In an effort to identify patients with uveal melanoma at high risk of metastasis, the authors undertook correlation of gene expression profiles with histopathology data and tumour‐related mortality.
Methods
The RNA was isolated from 27 samples of uveal melanoma from patients who had consented to undergo enucleation, and transcripts profiled using a cDNA array comprised of sequence‐verified cDNA clones representing approximately 4000 genes implicated in cancer development. Two multivariate data mining techniques—hierarchical cluster analysis and multidimensional scaling—were used to investigate the grouping structure in the gene expression data. Cluster analysis was performed with a subset of 10 000 randomly selected genes and the cumulative contribution of all the genes in making the correct grouping was recorded.
Results
Hierarchical cluster analysis and multidimensional scaling revealed two distinct classes. When correlated with the data on metastasis, the two molecular classes corresponded very well to the survival data for the 27 patients. Thirty two discrete genes (corresponding to 44 probe sets) that correctly defined the molecular classes were selected. A single gene (ectonucleotide pyrophosphatase/phosphodiesterase 2; autotaxin) could classify the molecular types. The expression pattern was confirmed using real‐time quantitative PCR.
Conclusions
Gene expression profiling identifies two distinct prognostic classes of uveal melanoma. Underexpression of autotaxin in class 2 uveal melanoma with a poor prognosis needs to be explored further.
doi:10.1136/bjo.2007.116947
PMCID: PMC2001033  PMID: 17475713
3.  DIFFERENTIAL EXPRESSION IN CLEAR CELL RENAL CELL CARCINOMA IDENTIFIED BY GENE EXPRESSION PROFILING 
The Journal of urology  2008;181(2):849-860.
Objective
Gene expression profiling has been shown to provide prognostic information regarding patients with a solitary, sporadic RCC. There is no reliable way to differentiate synchronous renal metastases from bilateral primary tumors in patients with bilateral RCC. We present data using a custom kidney cancer cDNA array that can predict outcomes in patients with unilateral and bilateral RCC.
Methods
Fresh frozen tissue from 38 clear cell RCC (cRCC) was analyzed using a cancer cDNA array containing 3966 genes relevant to cancer or kidney development. Median follow-up was 5.3 years; cancer had recurred in 12 (43%) patients and 11 (39%) patients were deceased at last follow-up.
Results
Using a training dataset of 8 tumors, a 44-gene expression profile (GEP) distinguishing aggressive and indolent cRCC was identified. Of 29 single cRCC, 16 were predicted to be indolent and 13 aggressive by GEP. Recurrence-free survival at 5 years was 68% and 42% in these 2 groups (P=.032). cRCC classified as indolent or aggressive according to SSIGN score had 5-year recurrence-free survival of 78% and 42%, respectively (P=.021). In a cox proportional hazards analysis, GEP was not an independent predictor of recurrence-free survival after accounting for SSIGN score. GEP classification correlated with cancer-specific survival at 5 years in 4 of 4 patients with metachronous cRCC, but only 2 of 4 patients with bilateral synchronous cRCC.
Conclusions
GEP using a kidney cancer-relevant cDNA array can differentiate between aggressive and indolent cRCC. GEP results may be most useful in unilateral cRCC when results are discordant with predictions of tumor behavior based on standard clinicopathologic features. In addition, GEP can provide prognostic information that may help characterize tumors of unknown clinical stage, such as bilateral metachronous cRCC.
doi:10.1016/j.juro.2008.10.069
PMCID: PMC2706314  PMID: 19095258
Carcinoma; Renal Cell; Microarray; Prognostic algorithm (nomogram); Gene expression profile
4.  GPRC6A Null Mice Exhibit Osteopenia, Feminization and Metabolic Syndrome 
PLoS ONE  2008;3(12):e3858.
Background
GPRC6A is a widely expressed orphan G-protein coupled receptor that senses extracellular amino acids, osteocalcin and divalent cations in vitro. The physiological functions of GPRC6A are unknown.
Methods/Principal Findings
In this study, we created and characterized the phenotype of GPRC6A−/− mice. We observed complex metabolic abnormalities in GPRC6A−/− mice involving multiple organ systems that express GPRC6A, including bone, kidney, testes, and liver. GPRC6A−/− mice exhibited hepatic steatosis, hyperglycemia, glucose intolerance, and insulin resistance. In addition, we observed high expression of GPRC6A in Leydig cells in the testis. Ablation of GPRC6A resulted in feminization of male GPRC6A−/− mice in association with decreased lean body mass, increased fat mass, increased circulating levels of estradiol, and reduced levels of testosterone. GPRC6A was also highly expressed in kidney proximal and distal tubules, and GPRC6A−/− mice exhibited increments in urine Ca/Cr and PO4/Cr ratios as well as low molecular weight proteinuria. Finally, GPRC6A−/− mice exhibited a decrease in bone mineral density (BMD) in association with impaired mineralization of bone.
Conclusions/Significance
GPRC6A−/− mice have a metabolic syndrome characterized by defective osteoblast-mediated bone mineralization, abnormal renal handling of calcium and phosphorus, fatty liver, glucose intolerance and disordered steroidogenesis. These findings suggest the overall function of GPRC6A may be to coordinate the anabolic responses of multiple tissues through the sensing of extracellular amino acids, osteocalcin and divalent cations.
doi:10.1371/journal.pone.0003858
PMCID: PMC2585477  PMID: 19050760
5.  Identification of a Novel Extracellular Cation-sensing G-protein-coupled Receptor* 
The Journal of biological chemistry  2005;280(48):40201-40209.
The C family G-protein-coupled receptors contain members that sense amino acid and extracellular cations, of which calcium-sensing receptor (CASR) is the prototypic extracellular calcium-sensing receptor. Some cells, such as osteoblasts in bone, retain responsiveness to extracellular calcium in CASR-deficient mice, consistent with the existence of another calcium-sensing receptor. We examined the calcium-sensing properties of GPRC6A, a newly identified member of this family. Alignment of GPRC6A with CASR revealed conservation of both calcium and calcimimetic binding sites. In addition, calcium, magnesium, strontium, aluminum, gadolinium, and the calcimimetic NPS 568 resulted in a dose-dependent stimulation of GPRC6A overexpressed in human embryonic kidney cells 293 cells. Also, osteocalcin, a calcium-binding protein highly expressed in bone, dose-dependently stimulated GPRC6A activity in the presence of calcium but inhibited the calcium-dependent activation of CASR. Coexpression of β-arrestins 1 and 2, regulators of G-protein signaling RGS2 or RGS4, the RhoA inhibitor C3 toxin, the dominant negative Gαq-(305–359) minigene, and pretreatment with pertussis toxin inhibited activation of GPRC6A by extracellular cations. Reverse transcription-PCR analyses showed that mouse GPRC6A is widely expressed in mouse tissues, including bone, calvaria, and the osteoblastic cell line MC3T3-E1. These data suggest that in addition to sensing amino acids, GPRC6A is a cation-, calcimimetic-, and osteocalcin-sensing receptor and a candidate for mediating extracellular calcium-sensing responses in osteoblasts and possibly other tissues.
doi:10.1074/jbc.M505186200
PMCID: PMC1435382  PMID: 16199532

Results 1-5 (5)