No evidence of mutation in the human PTC gene, responsible for nevoid basal cell carcinoma syndrome, in human primary squamous cell carcinomas of the esophagus and lung

The high frequency of loss of heterozygosity that has been observed on the distal region of the long arm of chromosome 9 in squamous cell carcinomas of esophagus, lung, uterus, and head and neck indicates the presence of a tumor suppressor gene(s) in this region. To investigate the possible role of the PTC gene on chromosome 9q22.3, that was identified as the cause of nevoid basal cell carcinoma syndrome, during carcinogenesis in esophagus and lung, we examined 20 esophageal squamous cell carcinomas and 10 squamous cell carcinomas of the lung for mutations in any coding exon of PTC. Using single-strand conformation polymorphism and direct sequencing, we detected no mutations other than two non-deleterious polymorphisms. Our results suggest that inactivation of some tumor suppressor gene(s) on 9q other than PTC contributes to the development of squamous cell carcinomas in these tissues.

Dilated cardiomyopathy: a genetic approach

Images

Sporadic medulloblastomas contain PTCH mutations

Nevoid basal cell carcinoma syndrome (NBCCS), or Gorlin's syndrome, is an autosomal dominant disorder that predisposes to developmental defects and various forms of cancer. PTCH was recently proposed as a candidate gene for NBCCS due to its frequent mutation in basal cell carcinomas, the cancer most often associated with this syndrome. Another NBCCS-associated cancer is medulloblastoma, a common central nervous system tumor in children. Most medulloblastomas, however, occur without indication of an inherited predisposition. We have examined 24 sporadic medulloblastomas for loss of heterozygosity (LOH) at loci flanking as well as within PTCH. In cases with LOH, single-strand conformational polymorphism and sequencing analysis were performed to determine the status of the remaining PTCH allele. Microsatellite analysis indicated LOH of PTCH in 5 of 24 tumors, and in three of these cases a mutation of the remaining allele was identified. Two of the mutations were duplication insertions, and the third consisted of a single base deletion. It is interesting that all three mutations occur in exon 17 of the PTCH gene. These data suggest that inactivation of PTCH function is involved in the development of at least a subset of sporadic medulloblastomas.

Bilineal acute leukemia of B and T lineage with a novel translocation t(9;17)(p11;q11)

We describe a case of bilineal leukemia in a 5-year old boy with a rare immunophenotype and the novel translocation t(9;17)(p11;q11) as the sole chromosomal abnormality. Two immunologically distinct blast cell subsets expressed T-markers (CD2, CD5, CD7) and common ALL markers (TdT, CD19, CD22, CD10), respectively. Both cell populations were CD34 negative. The patient, who presented with CNS leukemia, responded promptly to standard chemotherapy for lymphoblastic leukemia and remains in complete remission 20 months from diagnosis. Other translocations between chromosomes 9 and 17 have been infrequently reported in a variety of leukemias but as yet their biologic significance is unknown. The clinical course of this case suggests that t(9;17)(p11;q11) may not have an adverse influence on the disease outcome. However, the role of t(9;17) in the pathogenesis of this unusual lymphoid phenotype remains unresolved.

HMGI(Y) expression in human uterine leiomyomata. Involvement of another high-mobility group architectural factor in a benign neoplasm

Chromosomal rearrangements involving 6p21 have been observed in uterine leiomyomata and a variety of other benign tumors. The gene for HMGI(Y), a member of the high-mobility group (HMG) family of proteins, has been localized to 6p21. To determine whether rearrangements observed in this area alter HMGI(Y) expression, we analyzed HMGI(Y) DNA-binding activity in protein extracts from uterine leiomyoma and normal myometrium tissues. This report describes a uterine leiomyoma specimen with an inv(6)(p21q15). A genomic P1 clone that contains the HMGI(Y) region of chromosome 6 is found to span the inversion breakpoint by fluorescent in situ hybridization of metaphase chromosomes. Expression of HMGI(Y) protein in this leiomyoma specimen is increased dramatically as compared with the matching normal myometrial tissue. Elevated HMGI(Y) expression was also found in 8 of 16 leiomyomas without cytogenetically detectable chromosome 6p21 aberrations but not in any of the 9 matching myometrial tissues. Analysis of the genetic events involved in the pathobiology of these benign tumors will provide a basis for understanding the process of improper cellular growth and might be important in deciphering the multistep pathway of tumorigenesis.

Application of fluorescence in situ hybridization to detect residual leukemic cells with 9;22 and 15;17 translocations

We performed fluorescence in situ hybridization (FISH) upon 9;22 and 15;17 translocation-positive bone marrow cells to monitor the clinical course of 46 patients with chronic myelocytic leukemia (CML) and nine with acute promyelocytic leukemia (AML M3) who received chemotherapy and/or bone marrow transplantation (BMT). M-BCR-ABL and PML-RAR alpha probes were used to detect translocations of t(9;22) and t(15;17), respectively. Signals from CML patients treated with interferon (17 patients) or BMT (29 patients) were 0.5-15% positive for the 9;22 translocation. Among nine M3 patients who received extensive chemotherapy or BMT, 1-5% were positive for the 15;17 translocation. A highly sensitive FISH procedure using both translocation probes and a whole chromosome Y probe was established and applied to eight sex-mismatched BMT patients (seven CML and one AML M3), in which 0.1-0.6% of signals positive for the specific translocations were detected. These results suggested that interphase FISH is powerful enough to identify minor cell populations of 9;22 or 15;17 translocations after therapy, as well as to detect specific chromosome abnormalities at diagnosis.

Deletion map of chromosome 9 and p16 (CDKN2A) gene alterations in neuroblastoma

We reported previously that loss of heterozygosity (LOH) on chromosomes 2q, 9p and 18q frequently occurs in neuroblastoma and that patients with 9p LOH in the tumors showed statistically significant association with an advanced stage of the disease and poor prognosis. To determine the role of chromosome 9 loss in neuroblastoma, we performed deletion mapping of chromosome 9 in 80 cases of neuroblastoma using 11 polymorphic microsatellite markers and a restriction fragment length porymorphism marker. LOH at one or more loci on chromosome 9 was detected in 33 of 80 cases (41%). Chromosome 9p was lost in 24 of 80 cases (32%), whereas chromosome 9q was lost in 18 of 80 cases (23%). There were two commonly deleted regions mapped to 9p21 between the D9S171 marker and the IFNB1 marker and 9q34-qter distal to the D9S176 marker. In addition, patients with LOH at 9p21 but not at 9q34-qter in the tumors showed statistically significant association with poor prognosis (P = 0.023). Because the commonly deleted regions at 9p21 includes the p16 (CDKN2A) gene, the status of the p16 gene was further examined in 80 fresh tumors and 19 cell lines of neuroblastoma. A missense mutation was detected at codon 52 in a fresh tumor. The p16 gene was not expressed in 13 of 19 cell lines (72%), and 5 of the 13 cell lines displayed methylation of the CpG island surrounding the first exon of the p16 gene. These results suggest that the p16 gene is a candidate tumor suppressor gene for neuroblastoma, and its inactivation may contribute to the progression of neuroblastoma.

Molecular cloning of the human methylthioadenosine phosphorylase processed pseudogene and localization to 3q28

Human methylthioadenosine phosphorylase (MTAP) is a purine and methionine metabolic enzyme present ubiquitously in all normal tissues, but often deleted in many types of cancer. The gene for this enzyme maps to chromosome 9 at band p21 where the cyclin-dependent kinase inhibitor genes for p16 and p15 also reside. During our efforts to clone this gene we also isolated a phage clone containing a processed pseudogene of MTAP. The sequence is 92% homologous to the MTAP cDNA, is flanked at its 3' end by a repetitive element, but does not possess a poly(A) stretch. We localized this processed pseudogene to band 28 on the long arm of chromosome 3 by fluorescence in situ hybridization. All 22 malignant cell lines with deletions at 9p21 screened possessed the pseudogene.

Paracentric inversion involving the long arm of chromosome 9 resulting in deletion of abl gene

We report on a new chromosomal finding in a newborn male with hypertelorism, apparently low-set malformed ears with patent canal, micrognathia with narrow high-arched palate, bilateral webbing of neck with low posterior hairline, widely spaced nipples, and complex heart anomalies. Initially, what appeared to be a simple paracentric inversion of the long arm of chromosome 9, that is, 46,XY, inv(9)(q31q34) by routine GTG-banding technique was later determined to be a paracentric inversion with deletion of the band 9q34.1 by FISH technique using an abl unique sequence DNA probe. Thus the cytogenetic diagnosis was modified to 46,XY,der(9) inv(9)(q31q34.1)del(q34.1). Nevertheless, the presence of telomeric repeat sequences in the inverted chromosome 9 suggests that either healing has occurred by adding [TTAGGG]n sequences to the non-telomeric end (q31) by the enzyme telomerase or telomeric sequences were not affected during this inversion process. This abnormality is a rare occurrence and has never been reported before either because of a high rate of lethality or it has been undetected by routine cytogenetic techniques. The other abnormal cases with apparent paracentric inversions could also have a complex nature with congenital anomalies associated with loss of "few" DNA sequences as exemplified here.

Point mutations can inactivate in vitro and in vivo activities of p16(INK4a)/CDKN2A in human glioma

Deletions of chromosomal region 9p21 are among the most common genetic alterations observed during the clonal evolution of high grade malignant gliomas. Structural and functional evidence has suggested that homozygous deletion involving CDKN2A (the genetic locus encoding the cyclin-dependent kinase inhibitor p16(NK4a)) is a mechanism of inactivation of this gene and that it can be a growth suppressor in human gliomas. However, the presence of other potential suppressor genes in the 9p21 region and the relatively large sizes of the deletions has made it difficult to be certain that the CDKN2A gene is their actual target. Here, we tested this hypothesis by determining the growth suppressive effects, cell cycle inhibitions, and the activities of seven naturally occurring glioma-derived CDKN2A alleles carrying point mutations and found that two of them were functionally compromised. To resolve discrepancies among the different existing functional assays, we developed an assay for p16(INK4a) function that allowed us to demonstrate that the expression of wild-type CDKN2A, but not alleles with inactivating mutations, prevents pRB phosphorylation in vivo in human glioma cells. These data suggest that CDKN2A is a critical target for mutational inactivation in human malignant gliomas.

Identification through bioinformatics of two new macrophage proinflammatory human chemokines: MIP-3alpha and MIP-3beta

An increasing number of proinflammatory peptides, known as chemokines, are constantly being described and characterized. Because of their proven biologic functions in allergy, AIDS and, in general, inflammatory processes, these proteins have recently gained more attention. In this study we report the identification through bioinformatics of two new human chemokines: MIP-3alpha and MIP-3beta. Both of them belong to the beta- or CC chemokine family. Expression studies indicate that MIP-3alpha is predominantly expressed in lymph nodes, appendix, PBL, fetal liver, fetal lung and several cell lines. However, MIP-3beta expression is restricted to lymph nodes, thymus and appendix. Interestingly enough, both chemokines manifested a pattern of expression strongly regulated by IL-10. In contrast with other CC chemokines, MIP-3beta maps to chromosome 9. Here we show the importance of bioinformatics to discover new molecules with possible therapeutic effects and regulatory functions.

Detection of the Mbcr/abl translocation in chronic myeloid leukemia by fluorescence in situ hybridization: comparison with conventional cytogenetics and implications for minimal residual disease detection

The correlation between the detection of the Philadelphia chromosome by conventional cytogenetics and the identification of Mbcr/abl translocation by fluorescence in situ hybridization (FISH) in both metaphase and interphase cells is prospectively analyzed in a group of 21 chronic myeloid leukemia (CML) patients. To gain insight into the sensitivity and specificity of the detection of the bcr/abl translocation by FISH, a group of 10 healthy volunteers was also studied. Our results show that for the detection of bcr/abl translocation in CML patients, FISH is more sensitive than conventional cytogenetics because it detects significantly higher proportions of cells carrying the translocation both in metaphase (P < .0002) and interphase nuclei (P < .003). Moreover, in the metaphases of the controls analyzed, no bcr/abl+ chromosome was detected that makes the colocalization of bcr and abl signals in the CML patients highly specific. Conversely, in control interphase nuclei, a small proportion of cells (ranging between 0% and 3%, mean value of 1.7% +/- 0.9%) displaying colocalization of both signals is usually detected. This limits, at least for the moment, the routine use of FISH for the detection of minimal residual disease in CML patients at levels lower than 10(-1).

Identification of three distinct tumor suppressor loci on the short arm of chromosome 9 in small cell lung cancer

Deletion at 9p21 is frequent in many tumor types. A candidate tumor suppressor gene, p16INK4a, was mapped to this region and is frequently inactivated by several different mechanisms in many tumor types, including non-small cell lung cancer, but not in small cell lung cancer (SCLC). p16 functions as a cyclin/CDK inhibitor to prevent phosphorylation of pRB. It has been demonstrated that most SCLCs have lost pRB but retained p16, and the inactivation of pRB excludes the inactivation of p16 and vice versa. To determine the potential existence of other tumor suppressor genes on the short arm of chromosome 9 in SCLC, we tested 46 primary SCLCs by microsatellite analysis. We found that more than 89% of the tumors exhibited loss of heterozygosity (LOH) at 9p with three distinct minimal deleted areas. Among those areas, LOH at 9p21 was most frequent (86%), with a peak at a marker 150 kb telomeric to p16INK4a. LOH was also observed in more than 50% of the tumors at two other regions, 9p22 and 9p13. Our data strongly suggest the presence of at least three novel tumor suppressor loci on 9p in SCLC, and further investigations to clone candidate tumor suppressor genes are warranted.

Biological and clinical significance of cytogenetic study on 100 acute lymphoblastic leukemia and 219 acute non-lymphoblastic leukemia

OBJECTIVE

To further investigate the role that cytogenetic may play in the diagnosis and prognosis of leukemia, a study was conducted in 319 acute leukemias.

METHODS

100 patients with acute lymphoblastic leukemia (ALL) and 219 patients with acute non-lymphoblastic leukemia (ANLL) were from Rui Jin Hospital, Xin Hua Hospital, Ren Ji Hospital and Shanghai Children's Hospital. Their cytogenetic data were analyzed together with those of morphology, immunology and clinical prognosis.

RESULTS

In ALL group, 48 cases were karyotypically normal whereas 52 cases revealed chromosomal changes, among which 32 had quantitative abnormalities and 20 had qualitative abnormalities. The translocation t(9; 22) was identified in 11 out of 20 cases of structural aberrations (55%). Specific structural aberrations t(9; 22) and t(8; 14) were detected to be related to B-lineage associated differentiation antigens and t(8; 14) also with ALL-L3 according to FAB classification. With regard to clinical prognosis, the survival rate of structural aberration subset decreased significantly compared with the normal karyotype subset (P < 0.05). However, no statistically significant difference was found between hyperdiploidy subset (not including near-triploidy) and normal karyotype subset (P > 0.75). In ANLL group, 80% of de novo patients and relapsed patients had chromosomal abnormalities. Importantly, structural aberrations accounted for 73% of these abnormalities and frequently corresponded to specific types of FAB classification. Relevant prognostic studies demonstrated that t(15; 17) subset had the best overall survival probability, followed by t(8; 21) and normal karyotype subset, while the numerical aberration subset showed a relatively poor prognosis.

CONCLUSION

Our data confirmed that cytogenetic study is important for the molecular study of the leukemogenesis. On the other hand, it also provides an independent parameter for prognosis in acute leukemia.

Dynamics of Sau3A in situ digestion of human chromosomes analyzed with computerized imaging

The differential DNA removal obtained after in situ digestion of human metaphase chromosomes with the restriction endonuclease Sau3A was analyzed on complete and partially digested nuclei using computerized imaging. The results obtained permit the discrimination of Sau3A-resistant chromosome regions (pericentromeric constitutive heterochromatin on chromosomes 3 and 9) from those partially digested (Yq12 and pericentromeric heterochromatin on other chromosomes), according to the digestion dynamics deduced from the grey intensity profile along each chromosome. This approach permits an accurate labelling of chromosome markers for the identification of genomes from different individuals. This is of special interest for the analysis of the chimeric status found in patients after allogenic bone marrow transplantation.

The reciprocal translocation t(9;16)(q22;p13) is a primary chromosome abnormality in basal cell carcinomas

The reciprocal translocation t(9;16)(q22;p13) was identified in three short-term cultured basal cell carcinomas (BCCs). The t(9;16) was the sole anomaly in one clone in two tumors and was accompanied by a second change that also affected the long arm of chromosome 9 in the third. In addition, other cytogenetically unrelated abnormal clones were also found in all three BCCs. The identification of t(9;16)(q22;p13) as a primary chromosomal abnormality in a subset of BCCs (we found it in 3 of 22 tumors) is especially intriguing against the background that the PTCH gene, which when mutated in the germ line presumably gives rise to the autosomal dominant basal cell nevus or Gorlin's syndrome, maps to chromosome band 9q22. None of the genes rearranged in the BCC-specific t(9;16)(q22;p13) translocation have been identified, but we hypothesize that the translocation represents the cytogenetic corollary of a tumorigenic recombination of PTCH with an as yet unknown gene in 16p13. If so, this would be the first time that a tumor suppressor gene causally involved in a hereditary cancer is shown to be frequently rearranged through a specific translocation in sporadic carcinomas of the same type.

Loss of heterozygosity on chromosome 9q21 (p16 gene) uncommon in soft-tissue sarcomas

Chromosome region 9p21 contains a tumor suppressor locus (p16) that may be involved in the genesis of several kinds of malignant tumors. To characterize the role of this gene in the development of soft-tissue tumors (STTs), we investigated the frequency of loss of heterozygosity (LOH) at this locus. DNA was obtained from 77 tumors and the peripheral blood of 23 of the patients with the tumors. Using one microsatellite marker distal to p16(D9S171) and one intragenic sequence-tagged site (STS) marker (c5.1), we observed LOH in only one liposarcoma and one malignant schwannoma (2.6%). Homozygous deletions of the p16 markers were not found. The osteosarcoma cell line MG-63 was used as a control for loss of the p16 gene. Because of the low LOH frequency, we hypothesize that the p16 gene is not essential for STT oncogenesis.

Fine mapping of five human skeletal muscle genes: alpha-tropomyosin, beta-tropomyosin, troponin-I slow-twitch, troponin-I fast-twitch, and troponin-C fast

In this paper the chromosomal localization of the human skeletal muscle genes Troponin-I slow-twitch (TNNI1), Troponin-I fast-twitch (TNNI2), and Troponin-C fast (TNNC2) and the refinement of the position for alpha-Tropomyosin (TPM1) and beta-Tropomyosin (TPM2) are reported. By radiation hybrid mapping, TPM1 was assigned to chromosome 15q22.1, TPM2 to chromosome 9p13.2-p13.1, TNNI1 to chromosome 1q31.3, TNNI2 to chromosome 11p15.5, and TNNC2 to chromosome 20q12-q13.11. The genomic distribution of these genes is discussed, with particular emphasis on the cluster organization of the Troponin genes.

[The detection of minimal residual disease by DEK/CAN chimeric m-RNA in a case of AML M2 with translocation t(6;9) (p23;q34) after chemotherapy and peripheral blood stem cell transplantation]

A 18-year old female with acute myelogenous leukemia (AML), M2 had translocation: t(6;9) (p23; q34). The patient entered into hematological complete remission after two courses of BHAC-DMP chemotherapy with disappearance of cytogenetic abnormality. However, minimal residual disease (MRD) detected with DEK/CAN chimeric m-RNA by reverse transcription polymerase chain reaction (RT-PCR) was continuously observed, although decreased quantitatively, following several courses of consolidation and intensification chemotherapies. MRD was detected also in the harvested peripheral blood stem cells (PBSC). Leukemia relapsed with the reappearance of t(6;9) 2 months after the subsequent peripheral blood stem cell transplantation (PBSCT). Leukemia became refractory to chemotherapy, and the patient died 5 months thereafter.

Fine mapping of the nail-patella syndrome locus at 9q34

Nail-patella syndrome (NPS), or onychoosteodysplasia, is an autosomal dominant, pleiotropic disorder characterized by nail dysplasia, absent or hypoplastic patellae, iliac horns, and nephropathy. Previous studies have demonstrated linkage of the nail-patella locus to the ABO and adenylate kinase loci on human chromosome 9q34. As a first step toward isolating the NPS gene, we present linkage analysis with 13 polymorphic markers in five families with a total of 69 affected persons. Two-point linkage analysis with the program MLINK showed tight linkage of NPS and the anonymous markers D9S112 (LOD = 27.0; theta = .00) and D9S315 (LOD = 22.0; theta = .00). Informative recombination events place the NPS locus within a 1-2-cM interval between D9S60 and the adenylate kinase gene (AK1).

Linkage analysis of Fanconi anaemia in Italy and mapping of the complementation group A gene

Fanconi anaemia (FA) is an autosomal recessive disease characterised by genetic heterogeneity, with at least five complementation groups (FA-A to FA-E). The FAC gene has been cloned and localised to 9q22.3. The most frequent defective gene, FAA, was recently mapped to chromosome 16q24.3, in a region of 10 cM between D16S498 and the telomere. Eleven FA-A and 16 unclassified Italian families were analysed by microsatellite markers. To define the localisation of the FAA locus further, microsatellites were analysed at 16q24. All the families were consistent with linkage, the highest lod score being observed with D16S1320. Evidence for common haplotypes was obtained in two genetic isolates from the Brenta basin and the Naples region. Autozygosity mapping and haplotype analysis suggest that the FAA locus is distal to D16S305.

Combining nuchal translucency with umbilical Doppler velocimetry for detecting fetal trisomies in the first trimester of pregnancy

OBJECTIVE

The aim of our study was to evaluate whether the combined use of umbilical artery pulsatility index (UAPI) and nuchal translucency (NT) measurements would be useful in the prediction of fetal chromosomal abnormalities at 10 to 13 weeks of gestation.

DESIGN

A prospective study.

POPULATION AND METHODS

Five hundred and fifty-three consecutive women with singleton pregnancies between 10 and 13 weeks of gestation, who underwent chorionic villus sampling at our institution. UAPI and fetal NT thickness were measured immediately before the invasive procedure. Pregnancies in which structural malformations had been detected by ultrasound were excluded.

RESULTS

Using the 95th centile and 3 mm as the cutoffs for UAPI and NT, respectively, the detection rate for all chromosomal anomalies was 84.2%, with a false positive rate (1-specificity) of 6.6%, a positive predictive value of 31.3%, and a negative predictive value of 99.4%. Out of the 553 tested pregnancies 502 had both parameters within the normal range and only three of them (0.6%) were chromosomally abnormal; in six of the eight cases (75%) in which both parameters were abnormal a chromosome anomaly was present. Of the 43 cases in which only one parameter was abnormal, 10 were chromosomally abnormal (23.2%).

CONCLUSIONS

Our results suggest that the presence of chromosomal anomalies may be strongly suspected when an increased NT thickness (NT > or = 3 mm) is associated with an abnormally high UAPI at 10 to 13 weeks of gestation. The number of cases studied is small, however, and these conclusions are tentative and preliminary. The value of a single measurement of NT and UAPI for screening purposes needs to be substantiated by further investigation.

Generation of small insert genomic FISH probes with high signal intensity suitable for deletion mapping

We have developed a method to generate FISH probes from small (2-4 kb) nonrepetitive genomic restriction fragments. The probes showed a high hybridization efficiency of up to 90% in metaphase cells from normal peripheral blood. With the use of these probes, homozygous as well as hemizygous 9p deletions were reliably identified in nine leukemia-derived cell lines.

Paracentric inversion of chromosome 9 with schizoaffective disorder

A 36-year-old man with schizoaffective disorder was found to have a de novo 46 XY inv (9) (q31.2q34.3). Phenotypical abnormalities are short stature, depressed nasal bridge, hypertelorism and slender shoulders. Paracentric inversion of chromosome 9 is a rare chromosome aberration. This case suggests a new candidate region related to schizoaffective disorder.

The gene for the naevoid basal cell carcinoma syndrome acts as a tumour-suppressor gene in medulloblastoma

Individuals with naevoid basal cell carcinoma (Gorlin) syndrome are at increased risk of developing medulloblastoma in childhood. We have shown that approximately 5% of patients with Gorlin syndrome will develop this complication in the first few years of life, and in addition 10% of patients with medulloblastoma diagnosed at age 2 years or under have Gorlin syndrome. One out of three medulloblastomas occurring in patients with Gorlin syndrome was shown to have lost the wild-type allele on 9q, indicating that the Gorlin locus probably acts as a tumour suppressor in the development of this tumour. We have also confirmed this role in a basal cell carcinoma (BCC) from the same individual. Information from these families would suggest that Gorlin syndrome is more common than previously recognized and may not always be diagnosed on clinical grounds alone even in middle life.