Vijay S. Tonk

Allelotyping demonstrates common and distinct patterns of chromosomal loss in human lung cancer types

Allelic loss is a hallmark of tumor suppressor gene (TSG) inactivation. We have allelotyped 29 paired lymphoblastoid and lung cancer cell lines derived from 11 patients with small cell (SCLC) and 18 patients with non‐small cell lung carcinomas (NSCLC). Statistical analysis indicated that a threshold of 30% separated non‐random allelic loss from the random genetic deletions of malignancy. We have identified non‐random allelic loss at 42 of 54 (78%) specific chromosomal regions examined, with 22 regions (52%) common between the two major lung cancer histologic types. There were 3 regions (7%) with allelic loss specific for SCLC and 17 regions (41%) specific for NSCLC. Furthermore, there were significant differences in loss of heterozygosity (LOH) frequencies between NSCLC and SCLC at 13 regions on eight chromosome arms (3p, 5q, 6q, 9p, 10q, 11p, 13q, and 19p). Eight homozygous deletions were present in seven cell lines at four regions, 3p12, 3p14.2, 9p21, and 10q23–25. We have also identified novel sites of chromosomal deletions. In particular, there was frequent loss at 11p13 in SCLC and loss at 6p21.3 and 13q12.3 in NSCLC. In this study, we demonstrate that a) non‐random allelic losses in lung cancer involve multiple regions; b) some losses are common to both NSCLC and SCLC subtypes, whereas others are subtype specific; c) there are genetic deletions at novel chromosomal regions; and d) several homozygous deletions have been noted. Our studies demonstrate the usefulness of continuous cell lines for detailed allelotyping, for comparing genetic abnormalities between SCLC and NSCLC, and for identifying homozygous deletions. Genes Chromosomes Cancer 21:308–319, 1998.

Evidence for a Turner Syndrome Locus or Loci at Xp11.2-p22.1

Turner syndrome is the complex human phenotype associated with complete or partial monosomy X. Principle features of Turner syndrome include short stature, ovarian failure, and a variety of other anatomic and physiological abnormalities, such as webbed neck, lymphedema, cardiovascular and renal anomalies, hypertension, and autoimmune thyroid disease. We studied 28 apparently nonmosaic subjects with partial deletions of Xp, in order to map loci responsible for various components of the Turner syndrome phenotype. Subjects were carefully evaluated for the presence or absence of Turner syndrome features, and their deletions were mapped by FISH with a panel of Xp markers. Using a statistical method to examine genotype/phenotype correlations, we mapped one or more Turner syndrome traits to a critical region in Xp11.2-p22.1. These traits included short stature, ovarian failure, high-arched palate, and autoimmune thyroid disease. The results are useful for genetic counseling of individuals with partial monosomy X. Study of additional subjects should refine the localization of Turner syndrome loci and provide a rational basis for exploration of candidate genes.

Aberrant methylation of TMS1 in small cell, non small cell lung cancer and breast cancer.

TMS1 (target of methylation‐induced silencing) is a CpG island‐associated gene that functions in the regulation of apoptosis and encodes a caspase recruitment domain, a recently described motif found in apoptotic signaling molecules. Recent evidence suggests that silencing of genes in the apoptotic pathway contribute to human carcinogenesis. We examined the DNA methylation status of the TMS1 promoter in lung and breast tumor tissues, tumor cell lines and nonmalignant tissues by methylation‐specific polymerase chain reaction (MSP) and its mRNA expression by reverse transcription PCR. Aberrant methylation of TMS1 was present in 70% (40 of 57) of small cell lung cancer (SCLC) cell lines and 41% (13 of 32) of SCLC tumor tissues, 48% (29 of 61) of non small cell lung cancer (NSCLC) cell lines and 40% (28 of 70) of NSCLC tumor tissues and 46% (12 of 26) of breast cancer cell lines and 32% (20 of 63) of breast tumor tissues. Methylation was absent in the peripheral blood lymphocytes and buccal epithelium from healthy volunteers, as well as in nonmalignant lung tissues and was rare in nonmalignant breast tissues 7% (2 of 30). DNA methylation was confirmed by sequence analysis and the methylation status correlated inversely with TMS1 RNA expression in 18 cell lines tested. RNA expression was restored by treatment with the demethylating agent 5‐aza‐2′‐deoxycytidine, in 4 of 4 methylated cell lines that lacked the TMS1 transcript. Our results suggest that methylation of TMS1 may play a role in the pathogenesis of small cell and non small lung and breast cancers.

Chronic eosinophilic leukemia and hypereosinophilic syndromes : Proposal for classification, literature review, and report of a case with a unique chromosomal abnormality

The idiopathic hypereosinophilic syndromes (HES) are rare hematologic disorders characterized by persistent eosinophilia with organ involvement that encompass a wide spectrum of clinical and hematological disease states. We propose a classification scheme to further delineate these patients, and present a case of a 45-year-old male with persistent eosinophilia, severe tissue and hematologic involvement, and trisomy 15. Although multiple cytogenetic abnormalities have been associated with hypereosinophilic syndromes, this is the first reported case where trisomy 15 is the sole chromosomal abnormality.

Genomic alterations that contribute to the development of isolated and non-isolated congenital diaphragmatic hernia

Background Congenital diaphragmatic hernia (CDH) is a life threatening birth defect. Most of the genetic factors that contribute to the development of CDH remain unidentified. Objective To identify genomic alterations that contribute to the development of diaphragmatic defects. Methods A cohort of 45 unrelated patients with CDH or diaphragmatic eventrations was screened for genomic alterations by array comparative genomic hybridisation or single nucleotide polymorphism based copy number analysis. Results Genomic alterations that were likely to have contributed to the development of CDH were identified in 8 patients. Inherited deletions of ZFPM2 were identified in 2 patients with isolated diaphragmatic defects and a large de novo 8q deletion overlapping the same gene was found in a patient with non-isolated CDH. A de novo microdeletion of chromosome 1q41q42 and two de novo microdeletions on chromosome 16p11.2 were identified in patients with non-isolated CDH. Duplications of distal 11q and proximal 13q were found in a patient with non-isolated CDH and a de novo single gene deletion of FZD2 was identified in a patient with a partial pentalogy of Cantrell phenotype. Conclusions Haploinsufficiency of ZFPM2 can cause dominantly inherited isolated diaphragmatic defects with incomplete penetrance. These data define a new minimal deleted region for CDH on 1q41q42, provide evidence for the existence of CDH related genes on chromosomes 16p11.2, 11q23-24 and 13q12, and suggest a possible role for FZD2 and Wnt signalling in pentalogy of Cantrell phenotypes. These results demonstrate the clinical utility of screening for genomic alterations in individuals with both isolated and non-isolated diaphragmatic defects.

ABERRANT METHYLATION OF THE CYCLIN D2 PROMOTER IN PRIMARY SMALL CELL, NONSMALL CELL LUNG AND BREAST CANCERS

DNA methylation alteration of several genes contributes to human tumorigenesis. Cyclin D2, a member of the D‐type cyclins, is implicated in cell cycle regulation and malignant transformation. In our study, we examined the methylation status of the cyclin D2 promoter in small cell lung cancer (SCLC), nonsmall cell lung cancer (NSCLC), breast tumors and tumor cell lines. We observed that aberrant methylation of cyclin D2 was present in 32 of 56 (57%) SCLC cell lines, 7 of 32 (22%) SCLC tumor tissues; 25 of 61 (47%) NSCLC cell lines, 19 of 48 (40%) NSCLC tumor tissues; 18 of 30 (60%) breast tumor cell lines and 19 of 63 (30%) breast tumor tissues. Methylation was more frequent in the tumor cell lines compared to the primary breast and SCLC tumors (p = 0.007 and p = 0.001, respectively). Methylation was rare in the control tissue samples; 0 of 12 peripheral blood lymphocytes; 0 of 12 buccal epithelial cells; 0 of 18 nonmalignant lung tissues and 3 of 28 (11%) nonmalignant breast tissues. Promoter methylation correlated with loss of transcript by reverse transcription PCR (RT‐PCR) in 9 of 11 (6 lung, 5 breast) tumor cell lines tested. Two cell lines that were not methylated also lacked expression, suggesting that other mechanisms of inactivation may be involved. Expression was restored by treatment with the demethylating agent, 5 aza 2′ deoxycytidine, in all 9 methylated cell lines. Our results confirm earlier reports in breast cancer and indicate that aberrant methylation of cyclin D2 may contribute to the pathogenesis of the 2 major types of lung cancers.

Moving towards a syndrome: a review of 20 cases and a new case of non‐mosaic tetrasomy 9p with long‐term survival

Tetrasomy 9p is a rare syndrome that has now been described in nearly a score of cases. We present a new case of i(9p) that presented to us early in infancy with significant dysmorphological features, including growth retardation, psycho‐motor delay, hemifacial microsomia, auditory canal atresia, high‐arched palate, bulbous nose, strabismus, epicanthic folds, congenital heart disease, dislocated hips, hypoplastic external genitalia, simian palmar creases, dysplastic nails and small digits. Chromosomal analysis revealed a 47,XX,idic(9)(q12) karyotype on GTG‐ and C‐banding studies on peripheral blood lymphocytes. Fluorescent in situ hybridization (FISH) studies confirmed the origin of the extra chromosome. A review of the literature and a comparative analysis of the several well‐documented cases of i(9p) revealed a pattern of recurring features, including ear malformations, skeletal and joint problems (especially dislocations), hypoplasia of nails and digits, palatal abnormalities, hypertelorism, urogenital anomalies and developmental retardation. In the light of this analysis, we feel that tetrasomy 9p will soon be considered a clinically recognizable syndrome.

Del (X)(p21.2) in a mother and two daughters with variable ovarian function

We report a family in which a woman with the mosaic karyotype 45,X/46,X,del(X)(p21.2) transmitted the deleted X chromosome to two daughters. The nature of the deletion was confirmed by fluorescent in situ hybridization (FISH). All three family members showed somatic Ullrich‐Turner syndrome features, but only one daughter had ovarian failure. These observations have implications for the diagnosis of Ullrich‐Turner syndrome and genotype/phenotype correlations of X chromosome deletions.

Trisomy 5p. A case report and review

Trisomy 5p is a clinically discernable syndrome with characteristic clinical features. To date more than 40 patients with trisomy for various regions of short arm of chromosome 5 have been reported. Here we report a case with complete trisomy 5p and present a review of the literature.

Case report: Denovo inherited 18p deletion in a mother-fetus pair with extremely variable expression, confirmed by fluorescence in situ hybridization (FISH) analysis

Denovo deletions of 18p without other associated rearrangement are uncommon. For such a deletion to profoundly affect the fetus of a near normal phenotypic carrier would be rarer. We present such a case in which the chance of a cryptic rearrangement was ruled out by fluorescence in situ hybridization (FISH) analysis. Possible explanations for wide variations in clinical expression are discussed.