Deletion Of Long Arm Research Articles

2 Morphological differentiation of hypocellular refractory cytopenia of childhood and severe aplastic anemia and clinical outcome

5q syndrome was first described in 1974 by Van den Berghe who reported the consistent association of the deletion of the long arm of chromosome 5 [del(5q)] with haematological abnormalities: macrocytosis, anaemia, normal or high platelet count and hypolobulated megakaryocytes in the bone marrow. The 5q deletion is typically a large interstitial deletion and contains a number of genes involved in haematopoiesis. The del(5q) is also commonly found in other MDS and AML (10–15% of all patients) and is widely believed to mark the location for a tumour suppressor gene(s), the loss of which may affect important processes such as growth control and normal haematopoiesis. However, studies have failed to identify mutations within the retained alleles, or potential submicroscopic homozygous deletions in the commonly deleted region (CDR) suggesting that either haploinsufficiency promotes the 5q syndrome, or that a retained tumour suppressor allele has undergone epigenetic inactivation. To enable progress towards understanding the 5q− syndrome and to provide a model for testing novel therapeutics we generated a mouse model for the human 5q− syndrome. Using Cre-loxP recombination to delete the syntenic regions in the mouse equivalent to the human 5q CDR we have generated a mouse model (deletion mice), with a deletion on chromosome 18 flanked by the Cd74 gene and Nid67 gene (removing an interval harbouring Nid67, Dctn4, Rbm22,Myoz3, Synpo, Ndst1, Rps14, Cd74). The mice display macrocytic anemia, prominent erythroid dysplasia and monolobulated megakaryocytes in the bone marrow, similar to the human disease. Notably, intercrossing of deletion mice with p53 mice resulted in a reversal of the observed deficit in hematopoietic progenitor cell development, thereby demonstrating for the first time the mechanistic involvement of p53 in 5q syndrome. Recent studies have indicated a role for the ribosomal protein Rps14 in the development of 5q syndrome, and taken in combination with our deletion of Rps14, suggest that 5q may be a new member of the expanding group of ribosomopathies. Our work also suggests a prominent role for p53 in promoting the 5q phenotype in mice and we have recently shown p53 up-regulation in bone marrow trephines from del(5q) patients. This novel mouse model will allow the investigation of new and existing therapeutics, specifically targeted against del(5q) abnormalities, and give further mechanistic insight into 5q− syndrome. 2 Morphological differentiation of hypocellular refractory cytopenia of childhood and severe aplastic anemia and clinical outcome I. Baumann, C. Niemeyer, M. Fuhrer, S. Behrendt, V. Campr, J. Csomor, I. Furlan, V. de Haas, G. Kerndrup, R.J. Leguit, P. De Paepe, P. Noellke, S. Schwarz. Department of Pathology, Hospital Boeblingen, Boeblingen, Department of Pediatrics and Adolescent Medicine, University of Freiburg, Freiburg im Breisgau, Department of Hematology and Oncology, Ludwig-Maximilians-University Munich, Munich, Germany; Department of Pathology, University Hospital Motol, Prague, Czech Republic; Department of Pathology, Semmelweis University, Budapest, Hungary; Dutch Childhood Oncology Group, The Hague, The Netherlands; Department of Pathology, Vejle Hospital, Vejle, Denmark; Department of Pathology, University Medical Center Utrecht, Utrecht, The Netherlands; Department of Pathology, Ghent University Hospital, Ghent, Belgium; Department of Pathology, University Medical Center Erlangen, Erlangen, Germany

P02-223 - Kleefstra syndrome: neuropsychiatric sequelae

IntroductionSubmicroscopic deletions of the distal long arm of chromosome 9q are relatively common and give rise to a clinically recognizable phenotype referred to as the Kleefstra Syndrome [OMIM 610253]. It was shown that haploinsufficiency of the EHMT1 (Euchromatic Histone Methyltransferase 1) gene is responsible for the core phenotype by identifying cases with intragenic EHMT1 loss of function mutations. Key features of the syndrome are mental retardation, childhood hypotonia and facial dysmorphisms. Congenital heart and renal defects, microcephaly, epilepsy, and behavioural problems are frequently present.ObjectivesDescription of the developmental, behavioural and neuropsychiatric characteristics in 4 middle aged patients with recently diagnosed Kleefstra syndromeAimsContributing to the putative behavioural phenotype of Kleefstra syndrome.MethodsDetailed neuropsychiatric and neuropsychological assessment.ResultsIn the 4 patients, conventional cytogenetic investigation showed normal karyotypes. With routine subtelomeric MLPA and additional 9q regional specific MLPA tests, a submicroscopic deletion of the long arm of chromosome 9 (9q34.3) was found. Both deletions comprised the EHMT1 gene, in agreement with the diagnosis of Kleefstra syndrome. In all patients a severe apathy and a marked dyssomnia were present. Although some motor symptoms could be assessed with a catatonia rating scale, these have to be considered as a consequence of the apathy and belong therefore not to the catatonic spectrum.ConclusionsKleefstra syndrome is constituted, in addition to its distinct phenotypic features, by a specific behavioural phenotype that comprises, apart from the absence of speech development, a specific sleep disturbance and severe apathy from the third decade on.

Letters to the Editor

1 September 2009 Dear Editor, C1q nephropathy associated with deletion of long arm of chromosome 7 A 9-year-old boy with known chromosome 7q31.2-q32 deletion was referred with 6 months of asymptomatic microhaematuria and recent development of proteinuria, lethargy and anorexia. He was initially admitted to a regional hospital with a skin infection, and microhaematuria was incidentally detected, with raised anti-DNAse-B and anti-streptolysin-O titer. A urinary tract ultrasound was normal. He represented 2 months later with lethargy and anorexia. Urinalysis showed proteinuria and haematuria, with borderline hypertension (110/80). He was transferred to our service for further investigation, which yielded normal results for serum C3, C4, ANF, Anti-ds-DNA, UEC, FBP, plasma calcium, magnesium, phosphate and coagulation profile. A urine albumin/creatinine ratio was 73.2 (range <2.5) and calcium/creatinine ratio of 0.24 (0.04–0.70). Renal biopsy showed mesangioproliferative changes, normal tubulointerstitial pattern and no pathological vascular changes. Immunofluorescence revealed diffuse global, predominantly mesangial immunoglobulin G (IgG) and C3 deposition with extension into the capillary loops in some glomeruli. There was moderate C1q and sparse immunoglobin A (IgA) deposition (Fig. 1). Immunofluorescence shows moderate C1q and sparse IgA deposition, with diffuse global IgG and C3 deposition (predominantly mesangial) extending into the capillary loops of some glomeruli. Electron microscopy showed diffuse mesangial proliferation with extensive electron dense deposits in the mesangium and peripheral subepithelial basement membrane, with tubuloreticular inclusions. The histological findings in the absence of clinical, haematological and immunological signs of lupus was consistent with a diagnosis of C1q nephropathy. He has remained asymptomatic with no need for immunosuppression to date. This boy has previously been diagnosed with a de novo deletion of chromosome 7q31.2-32 by G-banded karyotype. He has learning problems, attention-deficit disorder with hyperactivity, seizures, dental abnormalities, a nephropathy and Wolf–Parkinson–White syndrome (WPWS). Previous published cases of deletions with similar breakpoints have language impairment because of Forkhead box protein P2 gene involvement, developmental delay and dysmorphic features,1 but there are no reports of nephropathy or WPWS with this deletion. No specific gene has been implicated in C1q nephropathy. Lim et al. reported a 3-year-old boy with C1q nephropathy and a family history of Dent disease, with the X-linked CLCN5 gene mutation. The significance of Dent disease to the development of the C1q nephropathy is unknown.2 Genes associated with proteinuria and nephrotic syndrome include NPHS1, NPHS2, WT1, LAMB2 and PLCE1. There are no known genes linked with nephrotic syndrome in the 7q region. The NOS3 gene in the 7q36 region has been implicated in causing hypertension and microalbuminaemia. Genetic regions on chromosomes 7q, 18q and 22q, contain genes determining variations in urinary albumin excretion, or susceptibility to proteinuria in families who have type 2 diabetes3 Whether the C1q nephropathy in our patient is related to the chromosome deletion remains to be elucidated. It is possible that this may be a chance observation. C1q nephropathy was first described in 1985 by Jennette and Hipp4 who outlined criteria for diagnosis as C1q deposits in the mesangium on immunofluorescence, corresponding mesangial or paramesangial electron-dense deposits on electron microscopy, and no evidence of systemic lupus erythematosus. The underlying aetiology is unknown. Children with C1q nephropathy commonly present with nephrotic syndrome or proteinuria. Kersnik et al. reported 12 paediatric patients: eight presented with nephrotic syndrome, one with nephrotic range proteinuria and three with non-nephrotic proteinuria associated with microhaematuria, hypertension and renal insufficiency.5 Vizjak et al. report on 72 C1q nephropathy patients (28 children). Clinical presentations included asymptomatic haematuria and or proteinuria (22%), frequently relapsing nephrotic syndrome with minimal change disease (63%) and nephrotic syndrome in all focal segmental glomerular sclerosis (FSGS) patients.6 Hatae et al.4 examined the results of 2221 children aged 1–15 years who underwent renal biopsy between 1975 and 2002. Thirty were diagnosed with C1q nephropathy based on the criteria of Jennette and Hipp. The C1q patients were divided into asymptomatic urinary abnormalities (18) and nephrotic group (12). Light microscopy showed minimal change disease (MCD) in 73%, mesangial proliferative glomerulonephritis in 20%, and FSGS in 7%. The natural history of C1q nephropathy in children suggests a good prognosis where the histological findings are of MCD, while children with FSGS progress to end-stage disease. Children with C1q nephropathy presenting with nephrotic syndrome are less likely to respond to corticosteroids and relapse frequently.4, 6 In summary, this is the first report noting an association between a deletion on the long arm of chromosome 7 and C1q nephropathy, suggesting that the relationship needs to be further investigated if other cases are identified. The authors are grateful to Dr TJ Beattie (Renal Unit, Royal Hospital for Sick Children – Yorkhill, Glasgow, Scotland) for his editorial suggestions.

Clinical Utility of Multiparameter Flow Cytometry in the Diagnosis of 1013 Patients with Suspected Myelodysplastic Syndrome: Correlation to Cytomorphology, Cytogenetic, and Clinical Data.

Abstract 595▪▪This icon denotes an abstract that is clinically relevant.Diagnosis and classification of myelodysplastic syndromes (MDS) is based on cytomorpholgy (CM) and cytogenetics (CG). By the identification of MDS-related aberrant antigen expression multiparameter flow cytometry (MFC) may add important diagnostic information. Examples include an aberrant expression pattern of CD13 and CD16 in granulocytes, an aberrante expression pattern of HLA-DR and CD11b in monocytes and the expression of lymphoid markers on myeloid blasts (Haematologica 2009:94:1124). To evaluate the potential role of MFC in the diagnostic setting of MDS we analyzed 1013 cases with suspected MDS by CM, CG, and MFC in parallel. Cases were classified by CM as refractory anemia (RA, n=31, 3.1%), refractory anemia with ring sideroblasts (RARS, n=27, 2.7%), refractory cytopenia with multilineage dysplasia (RCMD, n=64, 6.3%), refractory cytopenia with multilineage dysplasia and ring sideroblasts (RCMD-RS, n=49, 4.8%), refractory anemia with excess of blasts 1 (RAEB-1, n=133, 13.1%), RAEB-2 (n=81, 8.0%), 5q- syndrome (n=24, 2.4%), chronic myelomonocytic leukemia (CMML, n=65, 6.4%), myelodysplastic syndrome unspecified (MDS-u, n=15, 1.5%), MDS borderline to acute myeloid leukemia (MDS/AML, n=6, 0.6%), MDS/myeloproliferative neplasia overlap (MDS/MPN, n=16, 1.6%), suspected MDS (n=225, 22.2%), reactive condition (n=266, 26.3%), and normal findings (n=11, 1.1%). Cytogenetic findings were normal karyotype (n=768, 75.8%), isolated deletion of long arm of chromosome 5 (del(5q), n=43, 4.2%), isolated aberrations of chromosome 7 (n=14, 1.4%), isolated trisomy 8 (n=30, 3.0%), isolated deletion of long arm of chromosome 20 (del(20q), n=21, 2.1%), complex karyotype (n=23, 2.3%), loss of Y-chromosome (n=43, 4.2%), other aberrations (n=71, 7.0%). Concordance between CM and MFC was 82.0% for diagnostic results in 788 cases with unequivocal CM. 277 of these 788 cases were classified by CM as not having MDS, 13 (4.7%) of which showed MDS-typical features by MFC. Additional 225 cases showed only minor dysplastic features by CM, 51 (22.7%) of which showed clear evidence of MDS by MFC. To further analyze the significance of MDS-related findings by MFC we then focused on cytogenetically aberrant cases without unequivocal MDS by CM. In 6/12 (50.0%) cases with no indication of MDS by CM and MDS-typical cytogenetic aberrations MFC revealed MDS characteristics. In another 11/23 (47.8%) cases with minor dysplastic features by CM and MDS-typical cytogenetic aberrations MFC revealed MDS characteristics. Furthermore, we compared blast counts as determined by CM and MFC and found a strong correlation (p<0.001) although the mean±SD percentage was higher as determined by CM as compared to MFC (4.67±4.18 vs. 3.78±2.97). Frequencies of aberrantly expressed antigens significantly differed between cases rated by CM as MDS (median number of aberrantly expressed antigens: 3), suspected MDS (1), and no MDS (0, p<0.001). In various cases MFC identified MDS-typical aberrant antigen expression in cell compartments not rated dysplastic by CM. Spearman rank correlation confirmed a highly significant relation between the number of aberrantly expressed antigens and IPSS (r=0.409, p<0.001). In 257 cases with data on overall survival (OS) the presence of MDS-related findings (≥3 aberrantly expressed antigens or a blast count >5% in MFC or a reduced side-scatter signal) resulted in significantly inferior 6-year-OS (68% vs. 100% p=0.008). The present analysis clearly demonstrates a diagnostic yield of MFC in addition to cytomorphology and cytogenetics in cases with suspected MDS. Disclosures:Kern:MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership. Schnittger:MLL Munich Leukemia Laboratory: Equity Ownership. Haferlach:MLL Munich Leukemia Laboratory: Equity Ownership.

Further delineation of 9q22 deletion syndrome associated with basal cell nevus (Gorlin) syndrome: Report of two cases and review of the literature

Basal cell nevus syndrome (BCNS; Gorlin syndrome) is an autosomal dominant disorder, characterized by a predisposition to neoplasms and developmental abnormalities. BCNS is caused by mutations in the human homolog of the Drosophila patched gene-1, PTCH1, which is mapped on chromosome 9q22.3. Nonsense, frameshift, in-frame deletions, splice-site, and missense mutations have been found in the syndrome. Haploinsufficiency of PTCH1, which is caused by interstitial deletion of 9q22.3, is also responsible for the syndrome. To date, 19 cases with interstitial deletion of long arm of chromosome 9 involving the region of q22 have been reported. We describe two unrelated patients with some typical features of BCNS associated with deletion of 9q21.33-q31.1 and determined the boundary of the deletion by fluorescence in situ hybridization (FISH) with bacterial artificial chromosome (BAC) clones. The results showed that the size of deletions is between 15.33 and 16.04 Mb in patient 1 and between 18.08 and 18.54 Mb in patient 2. Although the size and breakpoints were different from those of previously reported cases, the clinical features are common to patients with 9q22 deletion associated with BCNS. Delineation of the 9q22 deletions and further consideration of the genes responsible for the characteristic manifestations may provide insight into this newly recognized deletion syndrome.

Banding patterns in human glioma cell lines.

G- and C-banding techniques were employed in studies of 2 diploid-near-diploid and 2 near-triploid established glioma cell lines. The origin of the marker chromosomes (their number ranging from 5 to 11) included in the stemline karyotypes could be almost completely clarified. The present results and those in 3 previously studied glioma cell lines were combined in order to characterize the banding patterns in astrocytic gliomas. An analysis of the chromosomal representation revealed a karyotypic profile distinguished by an increased proportion of chromosomes Nos. 7 and 19, and a reduction of chromosomes Nos. 4 and 22 and most likely also Nos. 10 and 12. Three different types of recurrent marker chromosomes were observed: A marker 12q- with an interstitial long-arm deletion was seen in 2 cell lines; a marker 13q- with a distal long-arm deletion occurred in 2 cell lines; a marker 14q- with a distal long-arm deletion was found in 3 cell lines. A study. of the distribution of breakpoints (as deduced from banding analyses of all different marker types found in all cell lines) showed a preferential involvement of certain chromosome types and also a clustering of the breakpoints in certain regions of several chromosome types. The numerical and structural observations in the glioma cell lines were interpreted as indicating the existence of several, possibly many, different karyotypic patterns in this type of neoplasm; the similarities between different cell lines were assumed to be related to their origin from the same tissue type rather than to any other factor, as for example the oncogenic agent(s).

The Multi-Copy Mouse Gene Sycp3-Like Y-Linked (Sly) Encodes an Abundant Spermatid Protein That Interacts with a Histone Acetyltransferase and an Acrosomal Protein1

Deletion analysis has established that genes on the Y chromosome are essential for normal sperm production in humans, mice, and Drosophila. In mice, long-arm deletions have an impact on spermiogenesis, with the most extensive deletions resulting in severe sperm head malformations and infertility. Intriguingly, smaller deletions are compatible with fertility but result in a distorted sex ratio in favor of females, and recently it was found that Y long-arm deletions are also associated with a marked upregulation of several X-encoded and Y-encoded spermatid-expressed genes. The mouse Y long arm encodes a number of distinct transcripts, each of which derives from multiple gene copies. Of these multicopy genes, the recently described Sly has been favored as the gene underlying the spermiogenic defects associated with Y long-arm deletions. To assess the candidacy of Sly, the expression of this gene was examined in the testis at the transcript and protein levels. Sly is transcribed after the first meiotic division in secondary spermatocytes and round spermatids and encodes two transcript variants, Sly_v1 and Sly_v2 (proteins referred to as SLY1 and SLY2). We raised an antibody against SLY1 which detected the protein in round and early elongating spermatids, where it is predominantly cytoplasmic. Yeast two-hybrid and coimmunoprecipitation studies demonstrated that SLY1 interacts with the acrosomal protein DKKL1, the histone acetyltransferase KAT5 (also known as TIP60), and the microtubule-associated protein APPBP2. Together, these data suggest SLY1 may be involved in multiple processes during spermiogenesis, including the control of gene expression and the development or function of the acrosome.

Interstitial deletion of chromosome 4

A 27-day-old girl child was admitted to our sick newborn care unit with neonatal seizure, piebald trait, corpus callosum dysgenesis and multiple dysmorphic features. Cytogenetic analysis revealed a female karyotype with interstitial deletion of the long arm of chromosome 4.

Aberrations in chromosomes associated with lymphoma and therapy‐related leukemia in benzene‐exposed workers

Epidemiological studies show that benzene exposure is associated with an increased incidence of leukemia and perhaps lymphoma. Chromosomal rearrangements are common in these hematopoietic diseases. Translocation t(14;18), the long-arm deletion of chromosome 6 [del(6q)], and trisomy 12 are frequently observed in lymphoma patients. Rearrangements of the MLL gene located on chromosome 11q23, such as t(4;11) and t(6;11), are common in therapy-related leukemias resulting from treatment with topoisomerase II inhibiting drugs. To examine numerical and structural changes in these chromosomes (2, 4, 6, 11, 12, 14, and 18), fluorescence in situ hybridization (FISH) was employed on metaphase spreads from workers exposed to benzene (n = 43) and matched controls (n = 44) from Shanghai, China. Aneuploidy (both monosomy and trisomy) of all seven chromosomes was increased by benzene exposure. Benzene also induced del(6q) in a dose-dependent manner (P(trend) = 0.0002). Interestingly, translocations between chromosomes 14 and 18, t(14;18), known to be associated with follicular non-Hodgkin lymphoma, were increased in the highly exposed workers (P < 0.001). On the other hand, translocations between chromosome 11 and other partner chromosomes that are found in therapy-induced leukemias were not increased. These data add weight to the notion that benzene can induce t(14;18) and del(6q) found in lymphoma, but do not support the idea that benzene induces t(4;11) or t(6;11). However, they do not rule out the possibility that other rearrangements of the MLL gene at chromosome 11q23 may be induced by benzene.

Clinical Relevance of Cytogenetics in Myelodysplastic Syndromes

Myelodysplastic syndromes (MDS) are a group of heterogeneous stem cell disorders with different clinical behaviors and outcomes. Conventional cytogenetics (CC) studies have demonstrated that the majority of MDS patients harbor clonal chromosome defects. The probability of discovering a chromosomal abnormality has been increased by fluorescence in situ hybridization (FISH), which has revealed that about 15% of patients with a normal chromosome pattern on CC may instead present cryptic defects. Cytogenetic abnormalities, except for the interstitial long-arm deletion of chromosome 5 (5q-), are not specific for any French-American-British (FAB)/World Health Organization (WHO) MDS subtypes, demonstrate the clonality of the disease, and identify peculiar morphological entities, thus confirming clinical diagnosis. In addition, chromosome abnormalities are independent prognostic factors predicting overall survival and the likelihood of progression in acute myeloid leukemia.

Patient with novel interstitial deletion of chromosome 3q13.1q13.3 and agenesis of the corpus callosum

Interstitial deletions of the proximal long arm of chromosome 3 are rare. Only eight previously reported patients have deletions involving the proximal segment of 3q. Of these patients, three had agenesis of the corpus callosum and one had holoprosencephaly. We report here a patient with a small unique interstitial deletion of the long arm of chromosome 3 spanning 3q13.1q13.3. This patient has agenesis of the corpus callosum, global developmental delay, and distinctive facial features of a small nose, anteverted nares, and broad nasal root. Our patient provides further evidence that a gene involved in corpus callosum development or neuronal migration may reside in this region.

Oesophageal atresia with a terminal deletion of chromosome 2q37.1

We herein report the case of a newborn girl with oesophageal atresia associated with cardiac and gastrointestinal anomalies, including patent ductus arteriosus, tracheomalacia, and gastro-oesophageal reflux with hiatus hernia. In addition, she had a terminal deletion of the long arm of chromosome 2, with a breakpoint of 2q37.1. The patient died following a cardiac arrest at 90 days of age. No cause of death was identified at autopsy.

Deletion of the Long Arm of Chromosome 6: Report on a New Case With Intractable Epilepsy

Interstitial deletions in the terminal region of chromosome 6 are rare. The deletion most often occurs de novo. Mental retardation is always described. The most characteristic manifestations are microcephaly, micrognathia, hypotonia, typical facial appearance, strabismus, and congenital heart defects. Although this chromosomal syndrome does not appear to have a distinctive phenotype, epileptic seizures are uncommon in affected individuals. We report on a novel finding in a patient with the 46 XX karyotype and del(6)(q25-q26) who developed intractable epilepsy.

Mapping of paternal-sex-ratio deletion chromosomes localizes multiple regions involved in expression and transmission

The paternal-sex-ratio (PSR) chromosome in the parasitic wasp Nasonia vitripennis is a submetacentric supernumerary (B chromosome). Males transmit PSR, but after fertilization it causes the loss of the paternal autosomes. Paternal genome loss caused by PSR results in the conversion of a female (diploid) zygote into a male (haploid) under haplodiploid sex determination. In this study, site-specific markers were developed to assay deletion derivatives of PSR. Both polymerase chain reaction and Southern hybridization were used to detect the presence/absence of 16 single-site markers on a set of 20 functional and nine nonfunctional deletion chromosomes. Based on the pattern of marker loss on the deletion chromosomes, the basic organization of PSR was revealed. Two sets of markers were deleted independently, apparently representing the two arms of the submetacentric chromosome. The presence or absence of specific regions was examined in relation to phenotypic characteristics of the deletion chromosomes; ability to cause paternal genome loss, and stability in mitotic cell divisions. Rather than identifying a single region on PSR as being responsible for PSR function, the results suggest that the retention of one of two chromosomal regions is sufficient for causing paternal genome loss. Furthermore, a region was identified that is tightly correlated with mitotic stability, as measured from chromosomal transmission rates. Functional chromosomes with short-arm deletions had high (approximately 100%) transmission rates, whereas functional chromosomes with long-arm deletions had low (approximately 85%) transmission rates.

Identification of candidate tumor suppressor genes from critical deletions of long arm of chromosome 6 in hematopoietic neoplasm

Deletion of the long arm of chromosome 6 has been frequently described in human lymphoid neoplasms as well as in other solid tumors, implicating the presence of tumor suppressor genes (TSGs) within this chromosomal segment. To isolate the relevant TSGs from the 6q14–23 region, we performed deletion analysis for a large panel of hematopoietic tumor samples using fluorescent in situ hybridization (FISH), employing more than 50 PAC/BAC clones mapped in 6q14–23 as probes. At least six critical regions (D1 to D6) existed within 6q14–23 that underwent overlapping deletions, but were discretely separated from each other, indicating multiple tumor suppressor loci might reside in this region. Deletions were most frequently observed in the D2 region that was flanked by the genetic markers D6S449 and AFMA084ZE9, followed by the D3, the region between D6S447 and WI-5694. Although attempts to identify candidate TSGs from the latter two regions involving sequencing analysis of both regions failed, we found another locus showing homozygous deletion telomeric to the D3 region by FISH analysis using additional probes. Of 106 cell lines examined, 3 had homozygous deletion in this locus, and finally, the Blimp1 gene was identified as the only gene that existed within the minimum overlapping homozygous deletion. Mutation analysis revealed that Blimp1 was mutated in 3 out of 106 primary lymphoid tumors. Our findings indicated that Blimp1 might be one of the target TSGs within 6q that was inactivated in human lymphoid neoplasms.

Partial deletions of long arm of chromosome 6: biologic and clinical implications in adult acute lymphoblastic leukemia.

Within 285 adult acute lymphoblastic leukemias (ALL) included in the multicenter GIMEMA 0496 trial and prospectively studied by conventional cytogenetics, 18 cases (6%) with long arm deletion of chromosome 6 (6q) were identified. These cases were divided into: (i) del(6q) only (n = 6); (ii) del(6q) plus other numerical and/or structural abnormalities (n = 8); (iii) del(6q) and other 'specific' translocations (n = 4). The biologic and clinical features of the patients carrying this anomaly, as well as their outcome, were compared with those of 267 patients without del(6q). A T cell phenotype was more frequently associated with del(6q) cases in general (P = 0.001) and particularly with cases presenting del(6q) as the isolated abnormality (P = 0.0027). No significant difference with respect to multidrug resistance (MDR)/P glycoprotein expression was observed between the two groups of patients (21% vs 28% of MDR-positive cases, respectively). A BCR-ABL fusion transcript was less frequently detected in cases with del(6q) (11%) compared with those without the anomaly (29%). p15 and p16 deletions were identified by Southern blot analysis in 21% of cases with del(6q) and in 26% of cases without del(6q). In this latter group, a T cell phenotype was less frequently associated with p15 and/or p16 deletion than in the group carrying del(6q) (36% vs 100% of cases, P = 0.011). Overall, patients with ALL and del(6q) had a high complete remission (CR) rate (83%); however, they had a lower 18 month event-free survival (31% vs 41%) and a higher relapse rate (70% vs 37%, P = 0.02) compared with patients without del(6q). To date, this is the largest series of adult ALL cases reported with del(6q) homogeneously treated, which have also been prospectively studied for MDR expression and for the detection of known fusion genes. This anomaly, as an isolated change, identifies a subset of cases with hyperleukocytosis (median WBC count 52 x 10(9)/l) and a strict correlation with a T cell phenotype. Overall, del(6q) seems to be associated with an unfavorable clinical outcome, although this finding will need to be confirmed by extended FISH analysis.

Association of the shrinkage of uterine leiomyoma treated with GnRH agonist and deletion of long arm of chromosome 7.

Specific chromosomal abnormalities, such as del(7q), t(12;14), 12 trisomy, or the rearrangement of 6p, are seen in approximately 30% of uterine leiomyomas despite their benign status. We investigated the association between the shrinkage of uterine leiomyomas treated with a GnRH agonist and the interstitial deletion of chromosome 7q, which is one of the most common chromosomal abnormalities in uterine leiomyomas. This study covered 29 women with uterine leiomyomas who were treated with a GnRH agonist before surgery. The volume of the largest myoma nodule was measured by means of MRI before and at 12 weeks after the beginning of GnRH agonist treatment, and the percentage of the reduction in volume was calculated. Genomic DNA was extracted from leiomyoma tissue and peripheral blood, and amplified by PCR using fluorescently-tagged oligonucleotide primers of twelve microsatellite loci on chromosome 7. The PCR products were analyzed for loss of heterozygosity (LOH) using an automated fluorescent DNA sequencer. Of the 29 informative tumors, five (17%) showed LOH with deletion of the common region, D7S491. The mean percentages of the reduction in volume of the largest myomas with LOH or without LOH were 32+/-13 and 18+/-58%, respectively (not significant). One tumor showing interstitial deletion of both alleles (homo-deletion) reduced in volume by 19%. Another tumor showing an extraband increased in volume by 13%. Although tumor specific chromosomal deletion suggested the existence of tumor suppressor genes in this region, there was no significant association between the shrinkage of uterine leiomyomas treated with a GnRH agonist and the interstitial deletion of chromosome 7q.

Interstitial deletion of the long arm of chromosome 4 [del(4)(q21.22q23)] and a liver tumor

Interstitial deletion of the long arm of chromosome 4 [del(4)(q21.22q23)] and a liver tumor

Terminal deletion of the long arm of chromosome 10: A new case with breakpoint in q25.3

Terminal deletion of the long arm of chromosome 10: A new case with breakpoint in q25.3

Loss of 18q predicts poor survival of patients with squamous cell carcinoma of the head and neck.

Tumor suppressor genes play an important role in normal growth regulation. Loss or inactivation of these genes has been implicated in the development of squamous cell cancer and progression of neoplasia. Previous studies in our laboratories have implicated chromosome 18 long-arm deletions as a possible marker of progression in head and neck squamous cell cancer (HNSCC). To test this hypothesis, we evaluated DNA from 67 HNSCC patients for loss of heterozygosity (LOH) at 18q loci, and for association of LOH with survival. Tumor and normal DNA were extracted from fresh tissue and paraffin blocks and were amplified by PCR using primers for three microsatellite repeat polymorphisms in 18q (D18S336, D18S34, and MBP). A total of 27 (40%) patients had LOH of 18q, and these patients had a statistically significantly poorer two-year survival compared to those without 18q LOH (30% vs. 63%; P = 0.008). In a Cox proportional hazards model in which time from diagnosis to death was the outcome variable, patients with 18q LOH had an unadjusted relative risk (RR) of death of 2.46 (P = 0.005). When 18q LOH was placed in a multivariate model controlling for possible confounders in the study, the RR for death was still elevated (RR = 2.10; P = 0.025). The observation of a prognostic association between 18q LOH and poor patient survival suggests that loss of an 18q tumor suppressor gene or genes is important in the progression of HNSCC.