Somatically acquired uniparental disomies (aUPDs) are frequent events in solid tumors and have been associated with cancer‐related genes. Studies assessing their functional consequences across several cancer types are therefore necessary. Here, we aimed at integrating aUPD profiles with the mutational status of cancer‐related genes in a tumor‐type specific manner. Using TCGA datasets for 1,032 gastrointestinal cancers, including colon (COAD), rectum (READ), stomach (STAD), esophageal adenocarcinoma (EAC) and esophageal squamous cell carcinoma (ESCC), we show a non‐random distribution of aUPD, suggesting the existence of a cancer‐specific landscape of aUPD events. Our analysis indicates that aUPD acts as a “second hit” in Knudson's model in order to achieve biallelic inactivation of tumor suppressor genes. In particular, APC, ARID1A and NOTCH1 were recurrently inactivated by the presence of homozygous mutation as a consequence of aUPD in COAD and READ, STAD and ESCC, respectively. Furthermore, while TP53 showed inactivation caused by aUPD at chromosome arm 17p across all tumor types, copy number losses at this genomic position were also frequent. By experimental and computationally inferring genome ploidy, we demonstrate that an increased number of aUPD events, both affecting the whole chromosome or segments of it, were present in highly aneuploid genomes compared to near‐diploid tumors. Finally, the presence of mosaic UPD was detected at a higher frequency in DNA extracted from peripheral blood lymphocytes of patients with colorectal cancer compared to healthy individuals. In summary, our study defines specific profiles of aUPD in gastrointestinal cancers and provides unequivocal evidence of their relevance in cancer.

Human chromosomes occupy distinct territories in the interphase nucleus. Such chromosome territories (CTs) are positioned according to gene density. Gene-rich CTs are generally located in the center of the nucleus, while gene-poor CTs are positioned more towards the nuclear periphery. However, the association between gene expression levels and the radial positioning of genes within the CT is still under debate. In the present study, we performed three-dimensional fluorescence in situ hybridization experiments in the colorectal cancer cell lines DLD-1 and LoVo using whole chromosome painting probes for chromosomes 8 and 11 and BAC clones targeting four genes with different expression levels assessed by gene expression arrays and RT-PCR. Our results confirmed that the two over-expressed genes, MYC on chromosome 8 and CCND1 on chromosome 11, are located significantly further away from the center of the CT compared to under-expressed genes on the same chromosomes, i.e., DLC1 and SCN3B. When CCND1 expression was reduced after silencing the major transcription factor of the WNT/β-catenin signaling pathway, TCF7L2, the gene was repositioned and mostly detected in the interior of the CT. Thus, we suggest a non-random distribution in which over-expressed genes are located more towards the periphery of the respective CTs.

Colorectal cancer (CRC) is characterized by specific patterns of copy number alterations (CNAs), which helped with the identification of driver oncogenes and tumor suppressor genes (TSGs). More recently, the usage of single nucleotide polymorphism arrays provided information of copy number neutral loss of heterozygosity, thus suggesting the occurrence of somatic uniparental disomy (UPD) and uniparental polysomy (UPP) events. The aim of this study is to establish an integrative profiling of recurrent UPDs/UPPs and CNAs in sporadic CRC. Our results indicate that regions showing high frequencies of UPD/UPP mostly coincide with regions typically involved in genomic losses. Among them, chromosome arms 3p, 5q, 9q, 10q, 14q, 17p, 17q, 20p, 21q and 22q preferentially showed UPDs/UPPs over genomic losses suggesting that tumor cells must maintain the disomic state of certain genes to favor cellular fitness. A meta-analysis using over 300 samples from The Cancer Genome Atlas confirmed our findings. Several regions affected by recurrent UPDs/UPPs contain well-known TSGs, as well as novel candidates such as ARID1A, DLC1, TCF7L2 and DMBT1. In addition, VCAN, FLT4, SFRP1 and GAS7 were also frequently involved in regions of UPD/UPP and displayed high levels of methylation. Finally, sequencing and fluorescence in situ hybridization analysis of the gene APC underlined that a somatic UPD event might represent the second hit to achieve biallelic inactivation of this TSG in colorectal tumors. In summary, our data define a profile of somatic UPDs/UPPs in sporadic CRC and highlights the importance of these events as a mechanism to achieve the inactivation of TSGs.

Colorectal cancer (CRC) mostly develops from a variety of polyps following mainly three different molecular pathways: chromosomal instability (CIN), microsatellite instability (MSI) and CpG island methylation (CIMP). Polyps are classified histologically as conventional adenomas, hyperplastic polyps, sessile serrated adenomas/polyps (SSA/P) and traditional serrated adenomas (TSA). However, the association of these polyps with the different types of CRCs and the underlying genetic and epigenetic aberrations has yet to be resolved. In order to address this question we analyzed 140 tumors and 20 matched mucosae by array comparative genomic hybridization, by sequence analysis of the oncogenes BRAF, KRAS, PI3K3CA and by methylation arrays. MSI was tested indirectly by immunohistochemistry (IHC) and a loss of MLH1, MSH2, MSH6 or PMS2 was assigned as high microsatellite instability (MSI-H), while low microsatellite instability (MSI-L) was defined as MGMT IHC negativity only. CIN was detected in 78% of all MSI-H CRCs, most commonly as a gain of chromosome 8. Methylation data analyses allowed classification of samples into four groups and detected similar methylation profiles in SSA/P and MSI-H CRC. TSA also revealed aberrant methylation pattern, but clustered more heterogeneously and closer to microsatellite stable (MSS) CRCs. SSA/P, TSA and MSI-H CRCs had the highest degree of promotor methylation (CIMP pathway). Chromosomal instability, in contrast to the established doctrine, is a common phenomenon in MSI CRCs, yet to a lower extent and at later stages than in MSS CRCs. Methylation analyses suggest that SSA/P are precursors for MSI-H CRCs and follow the CIMP pathway.

Background Aneuploidy, centrosome abnormalities and gene amplification are hallmarks of chromosome instability (CIN) in cancer. Yet there are no studies of the in vivo behavior of these phenomena within the same bladder tumor. Methods Twenty-one paraffin-embedded bladder tumors were analyzed by conventional comparative genome hybridization and fluorescence in situ hybridization (FISH) with a cyclin D1 gene ( CCND1 )/centromere 11 dual-color probe. Immunofluorescent staining of α, β and γ tubulin was also performed. Results Based on the CIN index, defined as the percentage of cells not displaying the modal number for chromosome 11, tumors were classified as CIN-negative and CIN-positive. Fourteen out of 21 tumors were considered CIN-positive. All T1G3 tumors were included in the CIN-positive group whereas the majority of Ta samples were classified as CIN-negative tumors. Centrosome clustering was observed in six out of 12 CIN-positive tumors analyzed. CCND1 amplification in homogeneously staining regions was present in six out of 14 CIN-positive tumors; three of them also showed amplification of this gene in double minutes. Conclusions Complex in vivo behavior of CCND1 amplicon in bladder tumor cells has been demonstrated by accurate FISH analysis on paraffin-embedded tumors. Positive correlation between high heterogeneity, centrosome abnormalities and CCND1 amplification was found in T1G3 bladder carcinomas. This is the first study to provide insights into the coexistence of CCND1 amplification in homogeneously staining regions and double minutes in primary bladder tumors. It is noteworthy that those patients whose tumors showed double minutes had a significantly shorter overall survival rate (p < 0.001).

The clinical behaviour of superficial bladder tumours is characterized by recurrence, which directs their clinical management. Identification of the molecular alterations critical for tumour recurrence and progression would enable a better management of patients with bladder cancer. The aim of this study was to assess the association between alterations in gene dosage and clinical parameters in patients with non-muscle invasive bladder carcinoma. To achieve this goal, the CCND1, CMYC, and EGFR genes and the 9p21 locus were analyzed by fluorescence in situ hybridization and Cyclin D1, p53, p21, and p16 proteins by immunochemistry in a tissue microarray composed of 152 Ta-T1 bladder tumours. Loss of 9p21 correlated with a decrease or absence of p16 protein expression as well as with an increase of Cyclin D1 and p21 protein expression. High gain of EGFR associated with high polysomy of chromosome 7 predicted shorter recurrence-free survival in non-muscle invasive tumours (OR = 2.29, 95%CI = 1.33–3.95, P = 0.003), and in particular in TaG2 tumours (OR = 5.06, 95%CI = 1.35–19.01, P = 0.016). Grade predicted shorter recurrence-free survival in T1G2 tumours (OR = 3.31, 95%CI = 1.04–10.49, P = 0.042). High gain of 9p21 associated with polysomy of chromosome 9 and high gain of CMYC predicted shorter progression-free survival in T1 tumours (OR = 7.17, 95%CI = 1.73–34.66, P = 0.014 and OR = 7.48, 95%CI = 1.85–30.29 P = 0.005, respectively). High gain of 9p21 remained as a single independent prognostic factor for tumour progression in T1G3 tumours (OR = 8.21, 95%CI = 1.36–49.31, P = 0.021). Tumour grade and CCND1 amplification associated with poor tumour specific survival in non-muscle invasive bladder tumours (OR = 4.32, 95%CI = 1.18–15.80, P = 0.027 and OR = 3.63, 95%CI = 1.11–11.95, P = 0.034, respectively), but this association was not significant when the analysis was performed separately in Ta and T1 tumours. High gain of EGFR is the main prognostic factor of tumour recurrence in superficial bladder tumours. High gain of 9p21 could be a good predictor for tumour progression in non-muscle invasive tumours, but especially in T1G3 tumours.

The CGH array technique allows for high-resolution genomic analysis, so it is possible to identify large-scale chromosomal imbalances and changes in the number of copies of regions even smaller than 1 Mb. SNP array technology, for its part, also provides information on loss of heterozygosity. In this study these techniques have been used to analyze 13 samples of colorectal carcinoma, in which each tumor was compared with adjacent normal mucosa of the same patient. In addition to the typical alterations of colon cancer, it has been observed that genomic structural variants contribute to generate imbalances of somatic origin in the tumor. These variants also appear in the sequences and breakpoints of some of the largest genes in the genome and common fragile sites. Moreover, the study shows that uniparental disomy is a common event in the developmental process of this kind of cancer. In conclusion, the technology employed constitutes a useful tool in identifying genes with impact on tumor development. Similarly, the relevance of regions rich in copy number variants and uniparental disomy in colorectal carcinogenesis is confirmed. Financial support: Plan Nacional SAF2007-64167, RTICC RD06/0020/1020.

Attention-deficit/hyperactivity disorder (ADHD) is the most common psychiatric condition with onset in childhood, and in more than 50% of cases it persists into adulthood as a chronic disorder. Over five million methylphenidate (MPH) prescriptions were issued in the USA in 2003, mostly for children. A previous report [R.A. El-Zein, S.Z. Abdel-Rahman, M.J. Hay, M.S. Lopez, M.L. Bondy, D.L. Morris and M.S. Legator Cytogenetic effects in children treated with methylphenidate, Cancer Lett. 230 (2005) 284–291.] described the induction of chromosome abnormalities by MPH in children treated for three months, contrary to most of the in vitro and in vivo studies reported since then. We present new relevant information concerning the cytogenetic effects of MPH in children and adults.We include a prospective sample of 12 children and 7 adults with a new diagnosis of ADHD and naive to MPH. We analyzed the cytogenetic effects on peripheral lymphocytes before and three months after starting MPH therapy. The cytogenetic analyses included a cytokinesis-block micronucleus (CBMN) assay, a sister chromatid exchange (SCE) analysis and the determination of chromosome aberrations (CA).Following the same strategy and analyzing the same cytogenetic endpoints that were investigated in the original report [R.A. El-Zein, S.Z. Abdel-Rahman, M.J. Hay, M.S. Lopez, M.L. Bondy, D.L. Morris and M.S. Legator Cytogenetic effects in children treated with methylphenidate, Cancer Lett. 230 (2005) 284–291.], we found no evidence of increased frequency of micronuclei, sister chromatid exchanges or chromosome aberrations induced by MPH in children and adult populations. MPH treatment of children and adults with ADHD resulted in no significant genomic damage (as suggested by the three endpoints studied), results that do not support a potential increased risk of cancer after exposure to MPH.

Background:The human chromosome 8p23.1 region contains a 3.8-4.5Mb segment which can be found in different orientations (defined as genomic inversion) among individuals.The identification of single nucleotide polymorphisms (SNPs) tightly linked to the genomic orientation of a given region should be useful to indirectly evaluate the genotypes of large genomic orientations in the individuals. Results:We have identified 16 SNPs, which are in linkage disequilibrium (LD) with the 8p23.1 inversion as detected by fluorescent in situ hybridization (FISH).The variability of the 8p23.1 orientation in 150 HapMap samples was predicted using this set of SNPs and was verified by FISH in a subset of samples.Four genes (NEIL2, MSRA, CTSB and BLK) were found differentially expressed (p,0.0005) according to the orientation of the 8p23.1 region.Finally, we have found variable levels of mosaicism for the orientation of the 8p23.1 as determined by FISH. Conclusion:By means of dense SNP genotyping of the region, haplotype-based computational analyses and FISH experiments we could infer and verify the orientation status of alleles in the 8p23.1 region by detecting two short haplotype stretches at both ends of the inverted region, which are likely the relic of the chromosome in which the original inversion occurred.Moreover, an impact of 8p23.1 inversion on gene expression levels cannot be ruled out, since four genes from this region have statistically significant different expression levels depending on the inversion status.FISH results in lymphoblastoid cell lines suggest the presence of mosaicism regarding the 8p23.1 inversion.

Comparative genomic hybridization and fluorescence in situ hybridization were used to define genetic changes associated with multifocal bladder cancer and to investigate whether the genetic relationship between synchronous urothelial tumors is similar to that observed within different parts of the same tumor. We investigated 8 synchronous urothelial tumors from 3 patients and macroscopically different parts of the same tumor from 2 other patients. The most frequent imbalances were gains of 1q, 2p, and 17q, and losses in 4q. The high number of chromosome imbalances detected in the present report confirms that a high level of chromosome instability could be characteristic of multicentric bladder tumors. Comparative genomic hybridization profiles obtained from independent tumors belonging to the same patient allowed us to elaborate cytogenetic pedigrees portraying the accumulation of chromosome alterations as a form of clonal evolution from a single precursor cell. The analysis of different macroscopic parts of the same tumor allowed us to detect chromosomal heterogeneity and to delineate intratumor clonal evolution. Some chromosome regions that appeared as a gain in one subpopulation were amplified in others indicating a genetic evolution process. Identical processes were observed in different tumors of the same patient. Expansion of chromosome gains and losses between different parts of the same tumor as well as in different tumors of the same patient was also observed. Our results not only provide further evidence of a clonal relationship between different synchronous bladder tumors but also show that the intratumor heterogeneity present in different subpopulations of the same tumor reproduces the behavior of independent synchronous tumors in a same patient.

In this study, we summarized cytogenetic and comparative genomic hybridization (CGH) results, mutation analysis of the MET gene, and immunohistochemistry results of tumors from three patients in the same family who were affected by hereditary papillary renal carcinoma (HPRC). All three patients showed germline mutations in the tyrosine kinase domain of the MET proto-oncogene, and developed bilateral and multiple papillary renal tumors. DNA mutation analysis showed an increased dosage of the mutant allele in six tumors from two patients but not in two tumors from the third patient. In addition to the recurrent chromosomal alterations found in papillary renal carcinomas, cytogenetic analyses revealed the presence of an identical chromosomal translocation, t(2;15)(q13;p11), in two different tumors from the same patient. Moreover, the same pattern of autosomal trisomies (+7, +12, +13, +17) was detected by CGH analysis in tumors from different siblings. Taking into account that the presence of an identical structural chromosomal aberration in two tumors and the gain of chromosome 13 are unusual chromosomal changes in this type of tumor, we can conclude that our results confirm those of other authors and suggest that the genetic predisposition to HPRC might predispose the acquisition of genomic alterations in specific chromosomes or chromosomal regions.

Most tumors show abnormal karyotypes involving either chromosome rearrangements and/or aneuploidies. The aim of our study is to measure the rate of both structural and numerical chromosome instability in two colorectal cancer cell lines: HCT116, and SW480 and its single subclones. To determine structural instability, we measured the nonclonal chromosome alterations of the last cell division by means of multicolor-fluorescence in situ hybridization (FISH). To quantify numerical instability, we used centromere-specific DNA probes to simultaneously detect chromosome loss and nondisjunctional events in binucleated cells obtained by cytokinesis-block micronucleus assay (CBMN). After clonal episodes, the structural chromosome instability rate increased significantly, confirming the large contribution of structural rearrangements to the heterogeneity of cancer cells. On the other hand, the aneuploidy rate was high and conserved in both the parental SW480 cell line and its subclones. The ability to differentiate chromosome loss and nondisjunction by the CBMN assay allowed us to conclude that no significant differences were detected among these events. Analysis of nucleoplasmic bridges, micronuclei, and nuclear blebs also demonstrated the differences among the structural instability rates of the parental cell line and its subclones. Overall, our results demonstrate the prevalence of structural over numerical chromosome instability in the subclones when comparing them with their parental cell line, confirming the contribution of ongoing chromosomal reorganizations in the generation of tumor cell heterogeneity.

The aim of the study was to investigate the spectrum and frequencies of chromosome aberrations induced by the exposure of different mouse spermatogenic germ cell stages to ionizing radiation. Male mice were exposed in vivo to X-rays. Chromosome aberrations were analyzed in first- and second-embryonic cleavages obtained from mating irradiated males with nonirradiated females at different periods after radiation exposure. A combination of telomeric and centromeric labeling as well as whole Y chromosome painting was used to characterize the rejoining pattern and the telomere status of the radiation-induced DNA breaks. The frequency of chromosome aberrations observed in eggs fertilized with sperm irradiated at the early spermatid stage was markedly higher than the frequency in eggs fertilized with sperm irradiated at the other spermatogenic stages when reference was made to the chromosome aberrations recovered in early embryos. At the first division postirradiation, distal rejoining of broken chromosome ends (in regard to the position of the centromere) was more frequent than proximal rejoining; thus compound acentric fragments were more frequently observed than dicentric chromosomes. The presence of additional telomere signals at the broken chromosome ends in mouse germ cells and early embryos, compatible with de novo formation of telomeres, was not frequent.

The expression of transgene loci in mammals often occurs in a heterocellular fashion resulting in variegated patterns of expression. We have examined the effect of chromosomal integration site, copy number, and transcriptionally activating sequences on the variegation of a keratin 5-lacZ (K5Z) construct in the stratified epithelia of transgenic mice. lacZ expression in these mice is always mosaic, and the beta-gal activity per cell is usually higher in the lines with a higher proportion of expressing cells. Similar constructs, in which cDNAs were exchanged by lacZ sequences, showed no variegation. Also, when a strongly active, nonvariegating construct was coinjected with K5Z, most transgenic lines showed an almost homogeneous lacZ expression. The comparison of transgene arrays of different copies inserted at the same locus (obtained by using a lox/Cre system) showed that the reduction of copy number does not lead to an increase in the proportion of cells that express the transgene. Finally, in most of the variegating or nonexpressing lines the transgenes were located both at intermediate positions and at peritelomeric regions in the long chromosome arms. These findings suggest that the probability and efficiency of expression of K5Z genes depend on both long range chromosomal influences and on sequences in the transgene array.

Centromere-specific DNA probes for chromosomes 4, 7 and 18 were used to simultaneously analyze chromosome loss, non-disjunction, breaks within the labeled region, and nucleoplasmic bridges induced by gamma rays in binucleated human lymphocytes. The doses used were 0, 1, 2 and 4 Gy, and approximately 1000 cells were scored per dose. Micronucleus frequency increased in a linear-quadratic fashion. For chromosome loss, significant increases were observed at 2 and 4 Gy, whereas for non-disjunction significant increases were observed at 1 Gy; thus non-disjunction allowed us to detect the effects of radiation at a lower dose than chromosome loss. The use of centromere-specific probes allowed discrimination between the clastogenic and aneugenic effects of ionizing radiation. The analysis of chromosome loss, not taking fragmented signals into account, ensures the detection of an aneugenic effect, which was not possible using pancentromeric probes. The frequency of chromosome breakage within the labeled regions was higher in nuclei than in micronuclei, suggesting an increase in the engulfment of chromosomal material by nuclei as a consequence of the presence of cytochalasin B in the cultures. Chromatin filaments connecting main nuclei, the so-called nucleoplasmic bridges, were observed in irradiated samples, and are a manifestation of rearranged chromosomes producing anaphase bridges.

Fluorescent in situ hybridization using three chromosome-specific centromeric human DNA probes was used to analyze the aneuploidy frequency in human-hamster two-cell embryos. With these techniques first mitotic division errors due to the effects of physical or chemical agents on human spermatozoa, such as non-disjunction and anaphase lag, can be easily detected. In control samples the estimated frequency of non-disjunction and anaphase lag was 3.4%. This assay can also detect premeiotic or meiotic errors. We estimated the same frequency (3.4%) for disomy, whereas monosomy was not found.

s of the 13th Annual Meeting of the ESHRE, Edinburgh 1997 homes for 3 min in a free play situation with their mothers when the infants were 4, 7, 13 and 21 weeks old.To have an indication of the whole family system, fathers were also videotaped when the infants were 21 weeks old.Once the recordings were completed, all videos were reviewed in detail and a coding system, which would objectively assess the style of the interaction, was developed.The following episodes were coded for the parents: caretaking, expression of affection, play involved, play not involved, talk involved, talk not involved, negative expression, intrusive behaviour and watching.For the infants, the following episodes were coded: vocal, play, attend, not attend, sleep, protest, avoid and vegetative (e.g.hiccups).The episodes were coded as events, and the onset and offset times of the particular event were recorded.Results: The caretaking behaviours of the mothers in the three groups showed different patterns of change over time.Virtually no caretaking behaviour was observed in mothers from the NIP group by the time the child was 21 weeks old, whereas mothers in both the IVF and INF groups continued to spend a considerable amount of time in caretaking.In the other parental episodes, no differences between the groups were observed.The play behaviour of the infants showed significant differences between the three groups (Kruskal-Wallis ANOVA: P = 0.012).Children in the NIP group played less than children in either the IVF (P = 0.021) or the INF group (P = 0.006).In all other infant episodes there were no observable differences between the three groups.Conclusion: Interaction between parents and IVF infants appears to develop along the 'normal' developmental path.However, the differences observed in parental caretaking and infant play behaviour between the NIP group and both groups who received infertility treatment need to be examined further and discussed.Drugs, poisons and the testis