Minimal Deletion Region Research Articles

DNA copy number alterations and expression of relevant genes in mouse thymic lymphomas induced by γ-irradiation and N-methyl- N-nitrosourea

The genetic mechanism for the development and progression of a lymphoma is unclear. This study investigated the alterations in the DNA copy number and the expression profiles of the genes located in the altered regions in mouse thymic lymphomas that were induced by two mutagens, γ-irradiation and N-methyl- N-nitrosourea (MNU). Microarray-based comparative genomic hybridization was used to precisely delineate the boundaries of the altered region. The copy number gains of chromosomes 4 and 5 were observed only in the radiation-induced lymphomas, and gains of chromosomes 10 and 14 were observed only in the MNU-induced lymphomas. Regional copy number losses in chromosomes 11, 16, and 19 appeared frequently in the radiation-induced lymphomas. The cancer-related genes Pten, Ikaros/Znfn1a1, Ercc4, and Top3b were located in the minimal deletion regions. In particular, the expression levels of the Pten, Top3b, and Ikaros genes were downregulated in both lymphoma groups, but the expression level of Ercc4 was downregulated only in the MNU group. This study also examined the expression levels of Sparc, Cxcl1, and Myc (synonym: c-Myc), which are located in the copy number gained chromosomes. Sparc was upregulated specifically in the radiation group, and Cxcl1 in the MNU group. c-Myc was upregulated in both groups. There was limited correlation between the DNA copy number profiles and the expression of the cancer-related genes in mouse lymphomagenesis. The chromosome aberrations and novel expression profiles of the cancer-related genes within the altered regions may provide important clues to the genetic mechanism for the development of lymphoma.

Analysis of Genetic Lesions in Atypical B-CLL by Pangenomic CGH-Arrays.

Among B-CLPD, characterized primarily by morphology and expression of cell surface markers, is is important to identify patients with CD5+ atypical B-CLL that is regarded as clinically more aggressive than typical B-CLL. However these cases are not well defined. To better characterize the genetic lesion observed in atypical B-CLL we have analysed a cohort of 40 patients by CGH microarrays.Study was made on 5 typical B-CLL and on 35 atypical B-CLL patients with either CD20dim or bright expression that do not express cyclin D1. All the patients with atypical B-CLL will be defined as the presence of an absolute B-CD5-positive lymphocytosis > 4 x 109/l and a RMH score < 4. DNA was extracted using QuiAmp kit according to manufacturer recommendations. 2μg of DNA was used in each hybridization experiment. DNA labeling was performed using Cy3dUTP and Cy5 dUTP respectively for control and tumoral sample respectively. CGH-arrays was performed using the 1 Mb Human genome micro-array from “arraygenomics” that contains 3400 BAC clones fully FISH mapped and end sequenced all printed in triplicate. Each experiment was made using two slides in dye swap method. Cy5 and Cy3 fluorescence intensities spot were quantified using Axon Scanner 4100 and Acuity Software. Data were imported into SpectralWare 2.0 software and Normalise Suite, version 2.0, Profiler from Squire lab.Results: Identification of known and previously uncharacterized copy number alterations (CNAs) in the a-B-CLL cells genome was made in all the cases. The CGH profiles revealed that a-B-CLL genome is highly rearranged harbouring large numbers of distinct copy-number aberrations (75 CNAs among 31 chromosomal regions were found). Some of these CNAs are recurrent across different samples, allowing the definition of minimal common regions (MCR) of amplification or deletion. The size of the CNAs was extremely variable from one Bac probe to complete chromosome gains or losses. Specifically, our dataset included the known gains of chromosome 12 (14 cases), and the known deletion at 11q23, 13q14.3, 17p region but also new region of interest as +3p, 3q22 to 3qter, 4pter to 4q35.2, 5p15, 6p25.3 to 6p22, 8q22 to 8q24, 15q15.3 to 15q26, 17q11 to 17qter, +18 and +19 for gains and 1p35,1, 1p33, 2q22.3, 3p26.3 to 3p21.3, 5q34, 6p25.3, 6q16, 6q25.3 to 6q27, 7q31.3 to 7q32.2, 8p23.3 to 8p12, 10q11.2 to 10q21.1, 10q21.3, 10q23.2 to 10q24, 11q22.3 to 11q24.2, 15q14 to 15q21, 16p11.2 to 16q21, 21q22.1 for the deletions.To further corroborate the above finding, we had performed conventional FISH analysis using known probes for del 13q, del 11q, trisomy 12, del 17p and correlate our results with conventional cytogenetic findings when they were available. In all the cases CGH-arrays findings were confirmed by fish analysis or karyotype. The above findings were confirmed also in few cases using the Agilent's Human Genome CGH Microarray 44K that contains over 40,000 probes. Our first results confirmed BAC arrays results. CGH-arrays appears to be very informative to detect lesion in B-CLPD and show the high frequency of genetic lesions in a-CLL. The biological impact of this lesions by transcriptome analysis on the same sample and the prognosis impact is in progress.

Minimal Region of Deletion on Chromosomal Arm 3p25.1-p25.2 in Uveal Melanoma

To the Editor: Parrella et al. ( [1][1]) have reported a novel minimal region of deletion (MRD) in uveal melanomas located on chromosome 3p25.1-p25.2. This is very interesting because in uveal melanoma, monosomy 3 is strongly correlated with metastatic disease ( [2][2]). As loss of one chromosome

Characterization of 8p21.3 chromosomal deletions in B-cell lymphoma: TRAIL-R1 and TRAIL-R2 as candidate dosage-dependent tumor suppressor genes

AbstractDeletions of chromosome 8p are a recurrent event in B-cell non-Hodgkin lymphoma (B-NHL), suggesting the presence of a tumor suppressor gene. We have characterized these deletions using comparative genomic hybridization to microarrays, fluorescence in situ hybridization (FISH) mapping, DNA sequencing, and functional studies. A minimal deleted region (MDR) of 600 kb was defined in chromosome 8p21.3, with one mantle cell lymphoma cell line (Z138) exhibiting monoallelic deletion of 650 kb. The MDR extended from bacterial artificial chromosome (BAC) clones RP11-382J24 and RP11-109B10 and included the tumor necrosis factor–related apoptosis-inducing ligand (TRAIL) receptor gene loci. Sequence analysis of the individual expressed genes within the MDR and DNA sequencing of the entire MDR in Z138 did not reveal any mutation. Gene expression analysis and quantitative reverse transcriptase–polymerase chain reaction (QRT-PCR) showed down-regulation of TRAIL-R1 and TRAIL-R2 receptor genes as a consistent event in B-NHL with 8p21.3 loss. Epigenetic inactivation was excluded via promoter methylation analysis. In vitro studies showed that TRAIL-induced apoptosis was dependent on TRAIL-R1 and/or -R2 dosage in most tumors. Resistance to apoptosis of cell lines with 8p21.3 deletion was reversed by restoration of TRAIL-R1 or TRAIL-R2 expression by gene transfection. Our data suggest that TRAIL-R1 and TRAIL-R2 act as dosage-dependent tumor suppressor genes whose monoallelic deletion can impair TRAIL-induced apoptosis in B-cell lymphoma.

Genomewide loss of heterozygosity and its clinical associations in non small cell lung cancer

We extensively allelotyped a panel of 71 microdissected primary surgically resected non small cell lung cancer (NSCLC) tumors to identify chromosomal regions that are likely to contain tumor suppressor genes (TSGs) or associated with clinicopathologic and prognostic effects. Loss of heterozygosity (LOH) was detected by genotyping of 177 microsatellite markers and correlation of LOH with clinicopathologic parameters and prognosis was analyzed. Twenty markers showed an LOH frequency greater than 48%, and 8 of them (2p23.3, 2p24.3, 2q35, 6p22.2, 7p14.3, 7p22.2, 17q24.3 and 21q22.3) were novel in NSCLC. The high LOH regions were confirmed by further aligning continuous LOH regions from another set of 24 NSCLC tissues and defining 7 minimal deletion regions ranging from 1.29 to 12.26 cM. The aberrations of 8 markers showed a significant correlation with alteration of p16 and Rb proteins, suggesting the gene(s) located in the chromosomal loss that may interact with p16/Rb pathway. In addition, markers specifically associated with smoking, histology types and tumor stages were identified and the linked candidate TSGs were suggested. For example, marker D1S1612 closely linked with Mig-6 gene was associated with smoking patients, squamous cell carcinoma patients and late-stage patients. Furthermore, 3 markers, D2S2968, D6S2439 and D7S1818, were significantly associated with poor prognosis of NSCLC patients using both univariate and multivariate Cox's regression analyses (p = 0.035, 0.022 and 0.006, respectively). These markers can potentially be used for early lung cancer detection, outcome measurement and the positional cloning of new TSGs whose loss of function contributes to NSCLC tumorigenesis.

Identification of a Novel Homozygous Deletion Region at 6q23.1 in Medulloblastomas Using High-Resolution Array Comparative Genomic Hybridization Analysis

The aim of this study is to comprehensively characterize genome copy number aberrations in medulloblastomas using high-resolution array comparative genomic hybridization. High-density genomic arrays containing 1,803 BAC clones were used to define recurrent chromosomal regions of gains or losses throughout the whole genome of medulloblastoma. A series of 3 medulloblastoma cell lines and 16 primary tumors were investigated. The detected consistent chromosomal aberrations included gains of 1q21.3-q23.1 (36.8%), 1q32.1 (47.4%), 2p23.1-p25.3 (52.6%), 7 (57.9%), 9q34.13-q34.3 (47.4%), 17p11.2-q25.3 (89.5%), and 20q13.31-q13.33 (42.1%), as well as losses of 3q26.1 (57.9%), 4q31.23-q32.3 (42.1%), 6q23.1-25.3 (57.9%), 8p22-23.3 (79%), 10q24.32-26.2 (57.9%), and 16q23.2-q24.3 (63.2%). One of the most notable aberrations was a homozygous deletion on chromosome 6q23 in the cell line DAOY, and single copy loss on 30.3% primary tumors. Further analyses defined a 0.887 Mbp minimal region of homozygous deletion at 6q23.1 flanked by markers SHGC-14149 (6q22.33) and SHGC-110551 (6q23.1). Quantitative reverse transcription-PCR analysis showed complete loss of expression of two genes located at 6q23.1, AK091351 (hypothetical protein FLJ34032) and KIAA1913, in the cell line DAOY. mRNA levels of these genes was reduced in cell lines D283 and D384, and in 50% and 70% of primary tumors, respectively. Current array comparative genomic hybridization analysis generates a comprehensive pattern of chromosomal aberrations in medulloblastomas. This information will lead to a better understanding of medulloblastoma tumorigenesis. The delineated regions of gains or losses will indicate locations of medulloblastoma-associated genes. A 0.887 Mbp homozygous deletion region was newly identified at 6q23.1. Frequent detection of reduced expression of AK091351 and KIAA1913 genes implicates them as suppressors of medulloblastoma tumorigenesis.

FRA16D common chromosomal fragile site oxido-reductase (FOR/WWOX) protects against the effects of ionizing radiation in Drosophila

Fragile sites are chromosomal structures that have been proposed to have a determining role in cancer-associated DNA instability. The human WWOX gene spans the FRA16D chromosomal fragile site, the common minimal region of homozygous deletion found in adenocarcinomas and three out of five translocation breakpoints in multiple myeloma. Transcripts from the alternatively spliced WWOX gene encode proteins with common N-terminal WW domains and variable homology to the oxidoreductase family of proteins. In this study, the Drosophila orthologue of the WWOX gene was identified and subjected to mutagenesis via homologous recombination. The resultant DmWWOX1 mutants were viable but exhibited an increased sensitivity to ionizing radiation. This radiation sensitivity was rescued by reintroduction and expression of either the wild-type Drosophila or human WWOX genes. Thus, the protective function of DmWWOX in response to irradiation in Drosophila is conserved with human WWOX (hWWOX). This is consistent with a protective role for hWWOX where aberrant expression, as a result of breakage at the associated fragile site, could contribute directly to cancer progression.

The del(2)(q32.2q33) deletion syndrome defined by clinical and molecular characterization of four patients

We report four patients with an interstitial deletion of chromosome 2q32 → 2q33. They presented similar clinical findings including pre- and postnatal growth retardation, distinct facial dysmorphism, thin and sparse hair and fair built, micrognathia, cleft or high palate, relative macroglossia, dacrocystitis, persisting feeding difficulties, inguinal hernia and broad based gait. All were severely mentally retarded. Three patients had a specific behavioral phenotype with hyperactivity and motor restlessness, chaotic behavior, happy-personality but with periods of aggression and anxiety, sleeping problems and self-mutilation. (head-banging). Array CGH and fluorescence in situ hybridization (FISH) allowed us to delineate the deletion size and showed that the four patients share a 8.1 Mb minimal deleted region. Reviewing additional nine case reports of patients with similar deletions showed striking phenotypic similarities which enabled the delineation of the 2q32.2q33 syndrome. Deletion of 2q32 has been also associated with the wrinkly skin syndrome (WWS) and isolated cleft palate. Although the patients presented here shared many aspects of WWS, they did not had the wrinkly skin. All patients had a cleft or high palate, most likely as a result of hemizygosity for SATB2. A potential commonly deleted interval of the three patients with behavioral problems, excluding the deletion in the patient without behavioral problems, is at most 0.5 Mb in size harboring only two genes.

Loss of heterozygosity and transcriptome analyses of a 1.2 Mb candidate ovarian cancer tumor suppressor locus region at 17q25.1‐q25.2

Loss of heterozygosity (LOH) analysis was performed in epithelial ovarian cancers (EOC) to further characterize a previously identified candidate tumor suppressor gene (TSG) region encompassing D17S801 at chromosomal region 17q25.1. LOH of at least one informative marker was observed for 100 (71%) of 140 malignant EOC samples in an analysis of 6 polymorphic markers (cen-D17S1839-D17S785-D17S1817-D17S801-D17S751-D17S722-tel). The combined LOH analysis revealed a 453 kilobase (Kb) minimal region of deletion (MRD) bounded by D17S1817 and D17S751. Human and mouse genome assemblies were used to resolve marker inconsistencies in the D17S1839-D17S722 interval and identify candidates. The region contains 32 known and strongly predicted genes, 9 of which overlap the MRD. The reference genomic sequences share nearly identical gene structures and the organization of the region is highly collinear. Although, the region does not show any large internal duplications, a 1.5 Kb inverted duplicated sequence of 87% nucleotide identity was observed in a 13 Kb region surrounding D17S801. Transcriptome analysis by Affymetrix GeneChip and reverse transcription (RT)-polymerase chain reaction (PCR) methods of 3 well characterized EOC cell lines and primary cultures of normal ovarian surface epithelial (NOSE) cells was performed with 32 candidates spanning D17S1839-D17S722 interval. RT-PCR analysis of 8 known or strongly predicted genes residing in the MRD in 10 EOC samples, that exhibited LOH of the MRD, identified FLJ22341 as a strong candidate TSG. The proximal repeat sequence of D17S801 occurs 8 Kb upstream of the putative promoter region of FLJ22341. RT-PCR analysis of the EOC samples and cell lines identified DKFZP434P0316 that maps proximal to the MRD, as a candidate. While Affymetrix technology was useful for initially eliminating less promising candidates, subsequent RT-PCR analysis of well-characterized EOC samples was essential to prioritize TSG candidates for further study.

MicroArrays comparative genomic hybridisation (aCGH) and response to neoadjuvant chemotherapy (CT) in breast cancer (BC)

607 Background: To develop comprehensive molecular predictors of response to neoadjuvant CT in breast cancer, we combined aCGH with expression profiling (cDNA arrays). Methods: Microdissected frozen breast core biopsies from 43 patients (pts) with operable BC were obtained before a neoadjuvant combination of doxorubicin-cyclophosphamide. In 17 pts, samples were also obtained 3 weeks after the first course of CT. aCGH was performed in 41 pts using ‘in-house’ microarrays containing ∼5.8K BAC clones, which comprise the whole genome in intervals of 1Mb. Data were analysed using CGH Analyser and an aCGH package built on S-Plus platform. We compared the aCGH results with expression profiling data of the same cases performed on an ‘in-house’ cDNA array with 4.6K clones. Results: 18/41 (44%) pts had a poor response to CT. aCGH results were validated by means of repeated independent biological replicates, chromosomal CGH and in situ hybridisation for HER2/neu (with a concordance of 97.5%). The most frequent genomic changes comprised gains of 1q (39%), 5p (34%), 8q (34%), 20q (24%), with the minimal regions of amplifications on 1q21.1, 1q32.1–32.2, 5p15.1, 8q22.1-q24.22, 20q13.12 and 20q13.13.q13.2, respectively. Losses were observed on 9p (24%), 5p (22%) and 16q (19%), with the minimal regions of deletion on 9p13.1-p12, 5p15.1, 16q22.1, 16q22.3 and 16q23.1-q23.3. Hierarchical clustering analysis based upon genetic alterations on all chromosomes showed that all but 1 pair of pre and post biopsies clustered together (correlation coefficients: 0.94–0.47) with a higher correlation in poor compared to good responders (p=0.013, Kolmogorov-Smirnov test). Gains on 8q23.3 and losses on 13q34 were the most significantly associated with poor response (p=0.01, Fisher exact Test). We detected correlations between amplifications and overexpressed genes in our predictive set for response. Conclusions: Specific chemotherapy-driven genomic changes were not detected following 3 weeks of treatment aCGH is a powerful method for the genome-wide detection of chromosomal imbalances and may be used in conjunction with expression profile data to build more biologically meaningful classifiers No significant financial relationships to disclose.

Congenital Diaphragmatic Hernia and Chromosome 15q26: Determination of a Candidate Region by Use of Fluorescent In Situ Hybridization and Array-Based Comparative Genomic Hybridization

Congenital diaphragmatic hernia (CDH) has an incidence of 1 in 3,000 births and a high mortality rate (33%-58%). Multifactorial inheritance, teratogenic agents, and genetic abnormalities have all been suggested as possible etiologic factors. To define candidate regions for CDH, we analyzed cytogenetic data collected on 200 CDH cases, of which 7% and 5% showed numerical and structural abnormalities, respectively. This study focused on the most frequent structural anomaly found: a deletion on chromosome 15q. We analyzed material from three of our patients and from four previously published patients with CDH and a 15q deletion. By using array-based comparative genomic hybridization and fluorescent in situ hybridization to determine the boundaries of the deletions and by including data from two individuals with terminal 15q deletions but without CDH, we were able to exclude a substantial portion of the telomeric region from the genetic etiology of this disorder. Moreover, one patient with CDH harbored a small interstitial deletion. Together, these findings allowed us to define a minimal deletion region of approximately 5 Mb at chromosome 15q26.1-26.2. The region contains four known genes, of which two--NR2F2 and CHD2--are particularly intriguing gene candidates for CDH.

Polymorphisms in GLTSCR1 and ERCC2 are associated with the development of oligodendrogliomas

Deletions of 19q have been associated with gliomas, especially oligodendrogliomas. In addition, cases with oligodendrogliomas with the 19q deletion have been observed to have a better survival compared with cases without the 19q deletion. The authors have previously described a 150-kilobase minimal deletion region in gliomas that maps to 19q13.33 and contains 3 novel candidate genes (GLTSCR1, EHD2, and GLTSCR2). The authors performed an association study using 141 cases with gliomas (61 cases with astrocytomas, 40 cases with oligodendrogliomas, 40 cases with mixed oligoastrocytomas) and 108 general controls. They evaluated 7 single nucleotide polymorphisms (SNPs) in 6 genes within and nearby the minimal 19q deletion region (ERCC2, RAI, ASE-1, ERCC1, GLTSCR1, and LIG1). The prevalence of a germline GLTSCR1-exon-1 T allele (SNP rs1035938) was 40% in cases with oligodendrogliomas compared with 27% in controls (P = 0.029), and the prevalence of an ERCC2-exon-22 T allele (SNP rs1052555) was 35% in cases with oligodendrogliomas compared with 18% in controls (P = 0.043). One high-risk and 1 low-risk haplotype were associated with oligodendroglioma development (P = 0.003 and 0.026, respectively). Cases with oligodendrogliomas with the 19q deletion had a significantly higher frequency of the GLTSCR1-exon-1 T allele compared with cases without the 19q deletion (P = 0.01). It was noteworthy that cases with gliomas who were homozygous for the GLTSCR1-exon-1 T allele had a significantly better survival: 77% and 68% survival at 2 and 5 years compared with 56% and 34% for other genotypes (P = 0.02, log-rank test). Multivariable analysis identified grade, age, and the GLTSCR1-exon-1 and ERCC2-exon-22 genotypes as independent predictors for survival. These results suggested that alterations in GLTSCR1 (or a closely linked gene) were associated with the development and progression of oligodendroglioma.

Characterization of 3p, 5p, and 3q in two nasopharyngeal carcinoma cell lines, using region-specific multiplex fluorescence in situ hybridization probes

Amplification of chromosome arms 3q and 5p and deletion of 3p were frequently detected in nasopharyngeal carcinoma (NPC) with comparative genomic hybridization and loss of heterozygosity studies. To identify the minimal amplified or deleted regions in these arms, structural aberrations in chromosome arms 3p, 3q, and 5p in two NPC cell lines, CNE1 and SUNE1, were studied with multiplex-color FISH (M-FISH) and chromosome region-specific probes (CRP). All CRPs, which were generated from microdissected DNA, were specific and strong in intensity, and sensitive enough to detect chromosome aberrations including translocations, deletions, and amplifications of target regions. In these two NPC cell lines, minimal regions of deletion and amplification were found at 3p12 and 3q26∼q27, respectively. On 5p, most of the regions were amplified as intact copies. Interregion translocations of these three arms were also observed. The amplification on 3q26∼q27 provided useful hints for further screening the minimal amplification at RP11-115J24 (3q26.2), containing candidate oncogene eIF-5A2. M-FISH with CRPs is thus not only useful in revealing a comprehensive picture of structural aberrations in target chromosomes, but also in narrowing down the minimal region for screening cancer-related genes.

Allelic Losses at 1p36 and 19q13 in Gliomas: Correlation with Histologic Classification, Definition of a 150-kb Minimal Deleted Region on 1p36, and Evaluation of CAMTA1 as a Candidate Tumor Suppressor Gene

Abstract Purpose: Allelic loss at 1p is seen in 70% to 85% of oligodendrogliomas (typically in association with 19q allelic loss) and 20-30% of astrocytomas. Because most 1p deletions in gliomas involve almost the entire chromosome arm, narrowing the region of the putative tumor suppressor gene has been difficult. To better define the histologic correlates of different patterns of 1p and 19q loss, we evaluated 1p/19q status in a large group of gliomas. This also allowed us to define a very small minimal deleted region (MDR) on 1p36. Experimental Design: Among 205 consecutive cases of glioma studied for 1p loss of heterozygosity (LOH), 112 tumors were evaluated for both 1p and 19q LOH using at least three polymorphic markers on 1p and 19q each. The latter group included both low-grade tumors (oligodendroglioma, diffuse astrocytoma, and “oligoastrocytoma”) and high-grade tumors (anaplastic oligodendrogliomas, anaplastic astrocytomas, anaplastic oligoastrocytomas). Tumors with small segmental 1p losses (defined as LOH at some loci with retention of heterozygosity at other loci) were studied using a more extensive panel of markers to define the 1p MDR. The candidate gene was screened for mutations and its expression was studied by qualitative and quantitative reverse transcriptase-PCR and Northern blotting. Results: Allelic losses on 1p and 19q, either separately or combined, were more common in classic oligodendrogliomas than in either astrocytomas or oligoastrocytomas (P &amp;lt; 0.0001). Classic oligodendrogliomas showed 1p loss in 35 of 42 (83%) cases, 19q loss in 28 of 39 (72%), and these were combined in 27 of 39 (69%) cases. There was no significant difference in 1p/19q LOH status between low-grade and anaplastic oligodendrogliomas. In contrast, no astrocytomas and only 6 of 30 (20%) oligoastrocytic tumors had combined 1p/19q loss. Although rare, 1p deletions were more often segmental in astrocytomas (5 of 6, 83%) than in oligodendrogliomas (3 of 35, 9%; P = 0.006). Eleven tumors (6 oligodendrogliomas or having oligodendroglial components, 5 purely astrocytic) with small segmental 1p losses underwent further detailed LOH mapping. All informative tumors in the oligodendroglial group and 2 of 3 informative astrocytomas showed LOH at 1p36.23, with a 150-kb MDR located between D1S2694 and D1S2666, entirely within the CAMTA1 transcription factor gene. Mutation analysis of the exons encoding conserved regions of CAMTA1 showed no somatic mutations in 10 gliomas, including 6 cases with and 4 cases without 1p LOH. CAMTA1 is normally expressed predominantly in non-neoplastic adult brain tissue. Relative to the latter, the expression level of CAMTA1 was low in oligodendroglial tumors and was further halved in cases with 1p deletion compared with those without 1p deletion (Mann-Whitney, P = 0.03). Conclusions: Our data confirm the strong association of combined 1p/19q loss with classic oligodendroglioma histology and identify a very small segment of 1p36 located within CAMTA1 that was deleted in all oligodendroglial tumors with 1p LOH. This MDR also overlaps the neuroblastoma 1p36 MDR. CAMTA1 shows no evidence of inactivation by somatic mutations but its expression is reduced by half in cases with 1p LOH, suggesting that the functional effects of CAMTA1 haploinsufficiency warrant further investigation.

Detailed deletion mapping of loss of heterozygosity on 22q13 in sporadic colorectal cancer

Both development and progression of malignancies occur as a multistep process, requiring the activation of oncogenes and the inactivation of several tumor suppressor genes. The loss of heterozygosity (LOH) of tumor suppressor genes is believed to play a key role in carcinogenesis of colorectal cancer (CRC). In this study, we analyzed the LOH of seven loci on chromosome 22q13 in an effort to identify candidate tumor suppressor genes involved in colorectal carcinogenesis. Matched tumor and normal tissue DNA were analyzed by PCR using fluorescence-labeled polymorphic microsatellite markers in 83 CRC patients. PCR products were eletrophoresed and LOH was determined by calculating the peak height acquired through computer software. Comparisons between LOH frequency and clinicopathological features were performed by chi2 test. P<0.05 was considered as statistical significance. The average LOH frequency of chromosome 22q13 was 28.38%. The highest LOH frequency was 64.71% on D22S1160 locus, and the lowest was 21.43% on D22S1141 locus. We detected two obvious minimal deletion regions: one between markers D22S1171 and D22S274, the other flanked by markers D22S1160 and D22S1149, each about 2.7 and 1.8 cm, respectively. None had lost in all informative loci. LOH frequency on D22S1171 is 50% on distal colon, which was higher than that on proximal one (P = 0.020); on D22S114 locus, none LOH event occurred in patients with liver metastasis, whilst 46.94% occurred in patients without liver metastasis (P = 0.008); on D22S1160 locus, LOH frequency in lymph nodes metastasis patients was 83.33%, which was much higher than 43.75% without lymph nodes metastasis ones (P = 0.016). There was no statistical significance between clinicopathological features and other loci. This study provides evidence of two minimal deletion regions, which may harbor putative tumor suppressor genes related to progression and metastasis in sporadic colorectal carcinoma on chromosome 22q13.

Cyclin-C: Analysis of a Candidate Tumour Suppressor Genes on 6q15-q21 in Malignant Lymphoid Cell Lines and Lymphoid Acute Leukemias.

Using FISH and LOH in ALL cases with microscopically visible deletions of the long arm of chromosome 6q, we previously defined a region of minimal deletion (RMD) in a spectrum of lymphoid malignancies and with other investigators have suggested that the region may harbour several tumour suppressor genes. (Sinclair et al 2004; Cancer Research , 64: 4089). 15 recognised genes were positioned in the RMD and three were found expressed in bone marrow: GRIK2, C6orf111 and Cyclin-C, the investigation of which is reported in this study.GRIK2 analysis. Combining published RMD in ALL with our own data, we extensively analysed GRIK2 in ALL patients carrying heterozygous 6q deletion. Although a paternally inherited non-silent mutation of GRIK2 was identified in one of 14 patients, we concluded that loss of one or more other genes in the 6q15-q21 region was likely to contribute to ALL pathogenesis.Cyclin-C (CCNC) analysis. Lymphoid cell lines without and with del (6q)(Peer, Molt-4 and NKL) were assessed for expression levels of C6orf111 and Cyclin-C and other candidate tumour suppressor genes within the region (FLASH, Q9NR58, Cx43, BACH2, BLIMP1, APG5L, TAK1 and AIM1) using real-time quantitative RT-PCR (RQ-PCR). While easily detectable in all other cell lines, no expression of CCNC was demonstrated in NKL (by RT-PCR and Western blotting), this in spite of the presence of at least one copy of the gene (as demonstrated by FISH using PAC P13743 which contains CCNC) suggesting that expression of the second allele was ablated through either micro-deletion, point mutation or epigenetic silencing. Expression levels of other candidate genes were similar, albeit with minor variations, in all cell lines. We further analysed expression of CCNC in whole PB and BM, a variety of haemopoietic cells isolated from PB and in 66 de novo ALL patients (9 T ALL; 48 B cell ALL (predominantly common ALL) and 9 other ALL). Expression was relatively high in all cell lines, intermediate in normal T-lymphocytes and low in other normal cells. Leukemic cells collected from diagnostic material from adult acute lymphoid malignancies showed a wide variation in levels of CCNC expression. To exclude the possibility that low expression in some cases may be due to the presence of a high proportion of normal cells CCNC levels were normalised against Ki67 expression (as an indicator of mitotic index) by RQ-PCR. At least 27 patients showed a CCNC level below the median value. Twenty-five cases showed value above the median value. Levels of expression of CCNC and Ki67 were correlated with survival, immunophenotype or other clinical parameters, but no statistically significant correlation was demonstrated.

Identification of a minimal deletion region on chromosome 5q in Chinese esophageal squamous cell carcinomas

The existence of unknown tumor suppressor gene(s) other than the APC gene has been hinted on 5q for esophageal squamous cell carcinoma (ESCC). In order to define minimal deletion intervals on 5q in ESCC and investigate the potential tumor suppressor gene(s), 9 microsatellite markers scattering the region from 5q22 to 5q35 were chosen for loss of heterozygosity (LOH) analysis in 50 primary ESCC from northern China. The results showed that six cases presented coexistence of LOH for three consecutive adjacent chosen markers, suggesting a minimal deletion region covering approximately 272 kb located on 5q23 from D5S1384 to D5S1505. It was a novel deletion region that was so far never reported in ESCC. Significant higher frequencies of LOH were observed in tumors with lower pathological grade at the locus D5S820 and with lymph node metastasis at the locus D5S408. The data suggested the possibility that one or more putative candidate tumor suppressor gene(s) on 5q23 might play an important role in the development and/or progression of ESCC.

A fluorescence in situ hybridization map of 6q deletions in acute lymphocytic leukemia: identification and analysis of a candidate tumor suppressor gene.

With the objective of identifying candidate tumor suppressor genes, we used fluorescence in situ hybridization to map leukemia-related deletions of the long arm of chromosome 6 (6q). Twenty of 24 deletions overlapped to define a 4.8-Mb region of minimal deletion between markers D6S1510 and D6S1692 within chromosome 6 band q16. Using reverse transcription-PCR, we found evidence of expression in hematopoietic cells for 3 of 15 genes in the region (GRIK2, C6orf111, and CCNC). Comparison between our own and published deletion data singled out GRIK2 as the gene most frequently affected by deletions of 6q in acute lymphocytic leukemia (ALL). Sequence analysis of GRIK2 in 14 ALL cases carrying heterozygous 6q deletions revealed a constitutional and paternally inherited C to G substitution in exon 6 encoding for an amino acid change in one patient. The substitution was absent among 232 normal alleles tested, leaving open the possibility that heterozygous carriers of such mutations may be susceptible to ALL. Although low in all normal hematopoietic tissues, quantitative reverse transcription-PCR showed higher baseline GRIK2 expression in thymus and T cells than other lineages. Among T-cell ALL patients, 6q deletion was associated with a statistically significant reduction in GRIK2 expression (P = 0.0001). By contrast, elevated GRIK2 expression was measured in the myelomonocytic line THP-1 and in one patient with common ALL. Finally, we detected significant levels of GRIK2 expression in prostate, kidney, trachea, and lung, raising the possibility that this gene may be protective against multiple tumor types.

Clinical and molecular analysis of combined hepatocellular-cholangiocarcinomas

Background/Aims Combined hepatocellular-cholangiocarcinoma (HCC-CC) show dual hepatocellular and biliary epithelial differentiation. To better understand the relations between cholangiocarcinoma (CC), HCC-CC and hepatocellular carcinoma (HCC), we screened for genetic alterations. Methods A series of nine CC, 15 HCC-CC and three separated HCC and CC lesions (‘collision tumors’) were screened for loss of heterozygosity (LOH) using 400 microsatellite markers and for p53 and β-catenin mutations. A comparison with a previously characterized series of 137 HCC was performed. Results In six cases of CC and HCC-CC, we identified TP53 gene mutations. A CTNNB1/β-catenin was identified in two patients presenting collision tumors, but no mutations were found in CC or in HCC-CC. A high level of chromosome instability in both CC and HCC-CC was found. Recurrent specific LOH were identified at 3p and 14q in more than 50% of the CC and the HCC-CC cases, whereas these chromosomal regions were deleted in less than 10% of the HCC cases ( P<10 −5). Minimal common regions of deletion (MCRD) were defined at 3p24-p14 and 14q24-q32, respectively. Conclusions These results suggest that combined HCC-CC are genetically closer to CC than HCC and common carcinogenesis pathways may be altered in HCC-CC and CC.

Clustering of minimal deleted regions reveals distinct genetic pathways of human hepatocellular carcinoma.

Systematic scan and statistical analysis of loss of heterozygosity (LOH) has been widely used to define chromosomal aberrations in various cancers for cloning of tumor suppressor genes and for development of prognostic markers. However, the establishment of novel strategies is needed, so that the nonrandom but heterogeneous chromosomal aberration data could provide significant insights into our understanding of molecular pathogenesis of cancers. After comprehensive allelotyping of recurrent allelic losses with 441 highly informative microsatellite markers and overlapping LOH regions on human hepatocellular carcinoma (HCC) chromosomes, 33 minimal deleted regions (MDRs) were revealed. Five and 15 of the 33 MDRs have physical intervals in less than 5 and 10 Mb, respectively, with the smallest MDR9p1 of 2.2 Mb located at 9p21.3-p21.2. Statistical and Kaplan-Meier survival analysis revealed a significant association between the loss of MDR15q1 (15q21.1-q22.2) and the HCC patient survival (adjusted P = 0.033). After cluster analysis of 33 MDRs that represented LOH profiles of each HCC tissue based on clinicopathological features and p53 mutations, two major genetic pathways, low-stage and advanced-stage HCC, were uncovered based on high concordance of MDR clusters. We propose that the definition of genome-wide MDRs on the cancer genome not only narrows down the location of existing tumor suppressor genes to facilitate positional candidate cloning and develop potential prognostic markers after statistical association of MDRs with clinicopathological features but also dissects genetic interactions and pathways of chromosomal aberrations in tumorigenesis.