Immaculada Ponsa

A Polymorphic Genomic Duplication on Human Chromosome 15 Is a Susceptibility Factor for Panic and Phobic Disorders

Anxiety disorders are complex and common psychiatric illnesses associated with considerable morbidity and social cost. We have studied the molecular basis of the cooccurrence of panic and phobic disorders with joint laxity. We have identified an interstitial duplication of human chromosome 15q24-26 (named DUP25), which is significantly associated with panic/agoraphobia/social phobia/joint laxity in families, and with panic disorder in nonfamilial cases. Mosaicism, different forms of DUP25 within the same family, and absence of segregation of 15q24-26 markers with DUP25 and the psychiatric phenotypes suggest a non-Mendelian mechanism of disease-causing mutation. We propose that DUP25, which is present in 7% control subjects, is a susceptibility factor for a clinical phenotype that includes panic and phobic disorders and joint laxity.

Comprehensive measurement of chromosomal instability in cancer cells: combination of fluorescence in situ hybridization and cytokinesis-block micronucleus assay

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.

Molecular patterns in the evolution of serrated lesion of the colorectum

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.

Nucleotide, cytogenetic and expression impact of the human chromosome 8p23.1 inversion polymorphism.

Background The human chromosome 8p23.1 region contains a 3.8–4.5 Mb 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.

Absence of cytogenetic effects in children and adults with attention-deficit/hyperactivity disorder treated with methylphenidate

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.

Non-disjunction and Chromosome Loss in Gamma-Irradiated Human Lymphocytes: A Fluorescence In Situ Hybridization Analysis Using Centromere-Specific Probes

Abstract Ponsa, I., Barquinero, J. F., Miró, R., Egozcue, J. and Genescà, A. Non-disjunction and Chromosome Loss in Gamma-Irradiated Human Lymphocytes: A Fluorescence In Situ Hybridization Analysis Using Centromere-Specific Probes. 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 γ 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.

Centrosome clustering and cyclin D1 gene amplification in double minutes are common events in chromosomal unstable bladder tumors

BackgroundAneuploidy, 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.MethodsTwenty-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.ResultsBased 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.ConclusionsComplex 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).

Genomic imbalances in urothelial cancer: intratumor heterogeneity versus multifocality.

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.

Comparative Genomic Hybridization Analysis Reveals New Different Subgroups in Early-stage Bladder Tumors

OBJECTIVES To classify bladder tumors according to their genomic imbalances and evaluate their association with patients outcome. METHODS Sixty-three superficially and minimally invasive bladder tumors were analyzed by conventional comparative genomic hybridization. Subtelomeric screening in 15 of these tumors was performed by multiplex ligation-dependent probe amplification. RESULTS Losses of 9q and 9p (32% and 25% of all cases, respectively) as well as gains of chromosomes Xq and Xp (28% and 25%, respectively) were the most frequent chromosome imbalances. Losses of 8p and gains in 1q and 8q were detected in >20% of cases. Tumors were classified into 3 groups according to their individualized pattern of gains and losses. The largest group was characterized by few chromosome imbalances, presenting 77% and 49% of the Ta and T1 tumors, respectively. Another group characterized by chromosomal gains, was composed of equal number of Ta and T1 tumors, with +1q and +17q gains being the most common imbalances. A minority group was characterized by chromosomal losses on 11q, 5q, and 6q. The multiplex ligation-dependent probe amplification study showed good correlation with comparative genomic hybridization results. With regard to the biological significance of this classification, a remarkable fact is that this minority group composed mainly of T1 tumors, showed a significant decrease in patient overall survival. CONCLUSIONS Our data suggest that superficial carcinomas of the bladder can be subdivided into a larger number of subclasses than had previously been expected. Our results also demonstrate a decreased survival among patients whose tumors show more genomic losses than gains.

Patterns of somatic uniparental disomy identify novel tumor suppressor genes in colorectal cancer

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.