Chromosomal aberrations and gene expression profiles in non-small cell lung cancer.

Alterations in genomic content and changes in gene expression levels are central characteristics of tumors and pivotal to the tumorigenic process. We analyzed 23 non-small cell lung cancer (NSCLC) tumors by array comparative genomic hybridization (array CGH). Aberrant regions identified included well-characterized chromosomal aberrations such as amplifications of 3q and 8q and deletions of 3p21.31. Less frequently identified aberrations such as amplifications of 7q22.3-31.31 and 12p11.23-13.2, and previously unidentified aberrations such as deletion of 11q12.3-13.3 were also detected. To enhance our ability to identify key acting genes residing in these regions, we combined array CGH results with gene expression profiling performed on the same tumor samples. We identified a set of genes with concordant changes in DNA copy number and expression levels, i.e. overexpressed genes located in amplified regions and underexpressed genes located in deleted regions. This set included members of the Wnt/beta-catenin pathway, genes involved in DNA replication, and matrix metalloproteases (MMPs). Functional enrichment analysis of the genes both overexpressed and amplified revealed a significant enrichment for DNA replication and repair, and extracellular matrix component gene ontology annotations. We verified the changes in expressions of MCM2, MCM6, RUVBL1, MMP1, MMP12 by real-time quantitative PCR. Our results provide a high resolution map of copy number changes in non-small cell lung cancer. The joint analysis of array CGH and gene expression analysis highlights genes with concordant changes in expression and copy number that may be critical to lung cancer development and progression.

The relationship of cognitive improvement after cognitive remediation with social functioning in patients with schizophrenia and severe cognitive deficits.

BACKGROUND: This study aims to examine the effects of change in neurocognition on functional outcomes and to examine predictors of change in social functions following a 12-week course of cognitive remediation in patients with schizophrenia and schizoaffective disorder with severe cognitive impairments. METHOD: Level of social functioning was assessed using a performance based measure of functional capacity (PSP) in patients prior to and after the completion of 12-week cognitive remediation treatment (CRT). Participants completed a neuropsychological battery (MCCB-MATRICS) and clinical measures at both time points. RESULTS: 63 subjects with a mean age of 41.4 (SD=12.2) and with 12.2years of education (SD=2.4) were enrolled. There were significant improvements in overall PSP score from baseline to endpoint (p=0.021) as well as in PSP domain A (socially useful activities) (p≤0.001), domain B (personal and social relationships) (p=0.009), and domain D (disturbing and aggressive behaviors) (p=0.003). There was a significant improvement in the composite MCCB score (p=0.020) and the Working Memory (p<0.046). Stepwise logistic regression yielded a significant association for baseline Visual Learning (Wald=6.537, p=0.011, OR=1.195), Speed of Processing (Wald=4.112, p=0.043, OR=0.850) and level of PANSS positive symptoms (Wald=4.087, p=0.043, OR=0.739) with PSP overall improvement. CONCLUSIONS: Faster speed of processing, better visual and verbal learning and less prominent positive symptoms were associated with greater functional improvement after a systematic cognitive intervention within a rehabilitative setting.

The U6 snRNA-encoding gene of the monogenetic trypanosomatid Leptomonas collosoma.

The U6 snRNA (U6) is the most conserved small nuclear RNA (snRNA) and apparently plays a central role in catalysis of the cis-splicing reaction. In trans-splicing, U6 may have an additional function. In the nematode trans-splicing system, a direct interaction between the U6 and spliced leader (SL) RNAs has been demonstrated, suggesting that U6 may serve as a bridge between the SL RNA and the acceptor pre-mRNA. To examine possible phylogenetic conservation of trypanosomatid U6 sequences that may interact with spliceosomal RNAs, we have cloned and sequenced the U6 gene from the monogenetic trypanosomatid Leptomonas collosoma (Lc). The Lc U6 deviates from the Trypanosoma brucei (Tb) RNA only in four positions located in the 5' stem-loop and the central domains. As in Tb, U6 is a single-copy gene and two tRNA genes, tRNAGln and tRNAIle, are found upstream to the gene. The tRNAs are differentially expressed; tRNAGln is transcribed in the opposite direction to U6, whereas tRNAIle is not transcribed. Possible base-pairing between U6 and the U2 and SL RNAs, similar to the interactions that take place in the nematode trans-splicing system, are proposed.

Studies on sperm chromosomes in patients with severe male factor infertility undergoing assisted reproductive technology treatment.

The aim of the study was to determine the rate of chromosome abnormalities in testicular sperm after intracytoplasmic sperm injection due to severe male factor infertility. The study groups included patient with non-obstructive azoospermia (n=9), obstructive azoospermia (n=10), Klinefelter's syndrome (n=5) and normal controls (n=6, groups I-VI, respectively). The mean serum levels of FSH 17.5+/-8.2 (P<0.05), 3.5+/-2.6, 29.8+/-13.0 (P<0.05) and 3.1+/-0.4 mIU/ml, respectively. The rates of chromosome abnormalities were 19.6% (P<0.001), 8.2% (P<0.001), 6.3 and 1.6%, respectively. Chromosomes X and Y were significantly more involved in the aneuploidy than chromosome 18 in groups I and II. The present findings demonstrate a linkage between gonadal failure (high serum FSH levels) and sperm chromosome abnormalities. Our findings may explain the increased incidence of perinatal sex chromosome abnormalities found in severe male factor patients. Patients with non-mosaic Klinefelter's syndrome have comparable risk for sex chromosomes aneuploidy as the rest of the patients with azoospermia. Therefore, genetic screening during pregnancy or before embryo replacement should be carefully considered in severe male factor patient following in vitro fertilization (IVF).

Congenital diaphragmatic hernia in a family segregating a reciprocal translocation t(5;15)(p15.3;q24).

Congenital diaphragmatic hernia (CDH) is a relatively common malformation of unknown cause with high mortality due to hypoplasia of the lungs and pulmonary hypertension. We studied a family in which two fetuses had CDH, and two pregnancies resulted in first trimester missed abortions. Both fetuses with CDH had an apparently normal karyotype. In a subsequent pregnancy, fluorescent in situ hybridization analysis of amniocytes showed a balanced translocation 46,XY, t(5;15) (p15.3;q24) also present in the mother and in a normal child, suggesting that the diaphragmatic hernia in the first two fetuses was caused by a cryptic unbalanced translocation. This hypothesis is supported by a previous observation of CDH in a distal deletion of 15q as part of a multiple congenital anomalies syndrome. It is suggested that a gene distal to 15q21 is important for the normal development of the diaphragm.

Use of interphase fluorescence in situ hybridization in third trimester fetuses with anomalies and growth retardation.

In the last few years, attention has been focused on the use of interphase fluorescence in situ hybridization (FISH) for prenatal diagnosis with chromosome-specific DNA probes in the second trimester. This technique is accurate, rapid, and detects the most common aneuploidies. We present a preliminary study using FISH technique on uncultured amniotic cells derived from 30 fetuses with ultrasonographic evidence of intrauterine growth retardation (IUGR) in the third trimester. Fifteen fetuses were males and 15 were females. Seven fetuses (23.3%) had abnormal chromosomal constitution: five (18.6%) had trisomy 21, one (2.35%) had trisomy 18, and one (2.35%) showed a mosaic trisomy 18. No abnormalities were detected in the other 23 fetuses. Amniocentesis combined with FISH appears to be a safe, rapid, and accurate alternative to blood sampling in the third trimester, reducing the clinical and emotional stress of the time required to complete chromosome analysis by routine cytogenetics.

Molecular cytogenetic studies in three patients with partial trisomy 2p, including CGH from paraffin-embedded tissue.

We report on three cases of partial trisomy 2p in which the identification and exact localization of the duplicated chromosome segment was possible only by application of molecular cytogenetic techniques. These included fluorescence in situ hybridization by use of wcp2, N-myc, and subtelomeric 2p probes and comparative genomic hybridization with DNA isolated from blood samples, frozen fetal tendon, and formalin fixed, paraffin-embedded fetal lung tissue. Two of the cases concerned fetuses of gestational week 20 and 24 with duplication of nonoverlapping terminal (2pter-->p24) and more proximal (2p25-->p23) segments and with distinctly different phenotypes. The third case was due to a de novo inverted duplication of 2p25-->p23, with loss of the subtelomeric region of 2p. This 53-month-old girl was a Bloom syndrome carrier. The patient had prenatal growth failure, borderline microcephaly, dilated lateral horns of the cerebral ventricles, transient cortical blindness, myopia, muscle hypotonia, and dilatation of the left renal collecting system. Dermal cysts were found on the glabella, the soles of both feet, and the vocal cord, causing respiratory embarrassment. Previously reported cases of pure trisomy 2p are reviewed, in an attempt to correlate clinical findings to overlapping regions in 2p. These cases illustrate the effectiveness of molecular cytogenetic methods in resolving subtle chromosomal aberrations in order to coordinate more accurately a chromosome regionspecific phenotype.

Caudal dysplasia sequence with penile enlargement: case report and a potential pathogenic hypothesis.

The clinical spectrum of caudal dysplasia sequence (CDS) is noted for its diversity. The origin of CDS remains unknown, though poorly controlled gestational diabetes has been implicated in some cases. Here we describe the case of a newborn with CDS associated with penile enlargement (PE). The main anomalies included anal atresia, agenesis of the kidneys and of the sacrococcygeal vertebrae, dysgenesis of lumbar vertebrae, and bilateral cryptorchidism. Penile enlargement (7 cm), a rather unusual finding, has so far not been reported in association with CDS. Chromosomal analysis failed, and the neonate died 30 min after birth. Comparative genomic hybridization analysis using stored DNA showed a balanced normal male DNA content, which negates chromosomal losses or gains as a cause of CDS and/or PE. PE due to virilizing-type adrenal hyperplasia, caused by common mutations in the genes encoding for the adrenal enzymes 21-hydroxylase and 11-hydroxylase, was ruled out. We report on a previously unpublished case of the coexistence of PE and severe CDS and propose a possible pathogenetic hypothesis of this association.

Comparative genomic hybridization analysis of radiation-associated and sporadic meningiomas.

Ionizing irradiation to the skull is a known risk factor for meningioma development. To gain insight into the molecular mechanisms that underlie radiation-associated meningioma (RAM), we characterized the somatic genetic alterations in 16 RAMs by using comparative genomic hybridization and compared the pattern of alterations with 17 nonradiation-associated meningiomas (non-RAM). Most tumors (29/33;87.9%) displayed at least one DNA copy number alteration, and 11 out of 33 (33%) exhibited four or more changes. The mean number of DNA copy number changes was similar in RAMs (2.4+/-1.9) and in non-RAMs (2.5+/-1.9). The most common DNA losses were noted in chromosome 22 (56.2% in RAM, and 47% in non-RAM) and chromosome 1 (37.5% in RAM and 35.3% in non-RAM), with no significant differences between the two groups. Noteworthy, gain in DNA copy number of chromosomes 8 and 12 was detected in two RAM tumors only. In conclusion, no significant differences were noted between RAMs and non-RAMs regarding the number of genetic changes and the extent and frequency of chromosomes 1 and 22 losses. These preliminary data suggest that the tumorogenic pathways of meningioma formation are similar, regardless of previous skull irradiation.

Sperm chromosome analysis and outcome of IVF in patients with non-mosaic Klinefelter's syndrome.

OBJECTIVE: The aim of the study was to determine the potential risk for fetal chromosomal anomalies in non-mosaic Klinefelter's syndrome patients undergoing IVF and intracytoplasmic sperm injection. DESIGN: Individually collected spermatozoa were isolated from wet testicular tissue preparations and fixed on glass slides using micromanipulation. Their nuclei were analyzed for chromosomes X, Y, and 18 by fluorescent in situ hybridization. SETTING: Assisted reproductive technology program. PATIENT(S): Consenting patients with non-mosaic Klinefelter's syndrome undergoing testicular biopsy and IVF (fresh specimens) or following such treatment (cryopreserved specimens). INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): The rates of numerical chromosome abnormalities for chromosomes X, Y, and 18 among spare testicular sperm and the pregnancy outcome following treatment. RESULT(S): Testicular sperm were found in 8 of 20 patients. Four couples became pregnant following embryo replacement. Sperm chromosomes were analyzed in five patients. One hundred and five sperm of 112 analyzed (93.7%) were normal with X to Y ratio of 50:55 (NS) respectively. Among the 112 sperm tested, seven (6.3%) demonstrated chromosomal abnormalities, of which five were related to the sex chromosomes and two to chromosome 18. One set of triplets, one set of twins, and two singletons (four males and three females) with normal karyotypes were born. CONCLUSION(S): Most of the testicular sperm retrieved from Klinefelter's syndrome patients demonstrates a normal pattern of sex chromosome segregation. Therefore, the risk of transmitting numerical sex chromosome abnormalities is relatively low and probably comparable with the rates found in other severe male factor infertility patient groups.

Sperm chromosome abnormalities in men with severe male factor infertility who are undergoing in vitro fertilization with intracytoplasmic sperm injection.

OBJECTIVE: To investigate the potential paternal contribution to the risk of fetal chromosomal anomalies after intracytoplasmic sperm injection (ICSI). DESIGN: Spermatozoa isolated from testicular tissue and ejaculated specimens of consenting patients undergoing testicular biopsy and ICSI were analyzed for chromosomes X, Y, and 18 by FISH. SETTING: Assisted reproductive technology program. PATIENT(S): Consenting patients undergoing testicular biopsy and ICSI, severe oligozoospermic patients, and normal fertile donors. INTERVENTION(S): None. MAIN OUTCOME MEASURE(S): The rate of chromosome abnormalities in testicular sperm with regard to the type of azoospermia and ejaculated sperm compared to healthy men. RESULT(S): The mean serum levels of FSH in the groups with nonobstructive azoospermia (n = 9), obstructive azoospermia (n = 10), severe oligozoospermia (n = 9), and the normal donors (n = 6) were 17.5 +/- 8.2 (P<.05), 3.5 +/- 2.6, 14.6 +/- 3.5 (P<.05), and 3.1 +/- 0.4 IU/mL, respectively. The corresponding rates of sperm chromosome abnormalities among these groups were 19.6% (P<.001), 8.2% (P<.001), 13.0% (P<.001), and 1.6%, respectively. The corresponding rates of disomy among these groups were 7.8% (12 of 153 spermatozoa), 4.9% (18 of 367), 6.2% (109 of 1,751), and 1% (5 of 500 spermatozoa), respectively. Errors in chromosomes X and Y were significantly more common than in chromosome 18. CONCLUSION(S): The present findings demonstrate a linkage between gonadal failure (high serum FSH levels) and the occurrence of sperm chromosome aneuploidies. Our findings may explain the increased incidence of sex chromosome abnormalities found after IVF in the severe male factor patient population. Genetic screening during pregnancy or before embryo replacement should be considered carefully.

Advanced FISH with directly labeled X, Y and 18 DNA probes as a tool for rapid prenatal diagnosis.

OBJECTIVE: To examine a rapid technique for identification and determination of fetal sex chromosomes and one autosome (chromosome 18) in uncultured amniotic fluids using fluorescence in situ hybridization (FISH) with directly labeled DNA probes and ignoring the use of proteinase K and Rnase. STUDY DESIGN: Twenty-five amniotic samples taken from pregnant women who were in their 18th gestational week and had advanced maternal age were studied for analysis of sex chromosomes and chromosome 18 with the FISH technique as well as standard cytogenetic analysis. RESULTS: Four hours after amniocentesis was performed, we identified the sex of the fetuses and disomy of chromosome 18 in a minimal sample of uncultured amniotic fluid by using directly labeled DNA probes for chromosomes X, Y and 18 (VYSIS) and ignoring the use of proteinase K and Rnase. CONCLUSION: The possibility of shortening the time required for identification of aneuploidies in a second-trimester fetus is useful in cases where fetal anomalies are ultrasonically diagnosed at a relatively advanced gestational age.

Prevention of posterior capsule opacification with the CO2 laser.

BACKGROUND AND OBJECTIVE: Posterior capsule opacification (PCO) is a common complication after cataract extraction, despite the modern surgical techniques and lenses being used for this procedure. Its prevention challenged many investigators, because the current treatment of choice, capsulotomy with Nd:YAG laser, is associated with sight-threatening complications. In the present study, the authors investigated two approaches of preventing PCO using the CO2 laser. MATERIALS AND METHODS: A 15-W CO2 laser with a 17- or 18-gauge hollow probe was used on 20 sheep eyes and 14 rabbit eyes. Lens extraction was done by phacoemulsification. In the equatorial treatment study, the anterior chamber was filled with either air or a viscoelastic substance, and laser burns were applied to the equator of the lens capsule and to the peripheral anterior capsule to destroy the epithelial cells. In the capsulotomy study, a primary posterior capsulotomy was created by delivering 1 to 3 laser shots to the capsule behind an implanted intraocular lens (IOL). RESULTS: The CO2 laser was satisfactory in sheep eyes after filling the anterior chamber with air. In rabbit eyes, however, it was technically impractical to work with air. Using a viscoelastic material to maintain the anterior chamber, the hollow probe of the CO2 laser becomes plugged up and therefore is unable to affect the ocular tissue. However, by combining viscoelastic and air pumping, both the destruction of the lens epithelial cells and the creation of a central posterior opening behind a capsular-fixated IOL was repeatedly achieved. CONCLUSION: Using the CO2 laser for destruction of lens epithelial cells and the creation of controlled posterior capsulotomy is feasible and practical. A different design of the probe (closed gauge) is required to enable it to operate clinically in a fluid or viscoelastic environment.

Cognition, psychosocial adjustment and coping in familial cases of velocardiofacial syndrome.

Velocardiofacial syndrome (VCFS) is characterized by both physical manifestations and neuropsychiatric disabilities. About 6-28% of cases are familial. The aim of the present study was to compare the clinical characteristics of subjects with familial and nonfamilial VCFS, with a special focus on cognitive and psychiatric disabilities. In addition, the complexities of coping with the disease in families in which both a parent and children are affected were highlighted in case vignettes. Sixteen patients from six families with VCFS were compared to 63 subjects with nonfamilial VCFS for physical parameters, IQ, and rate of major psychiatric disorders. After controlling for the effect of age, IQ was significantly lower in the familial compared to the nonfamilial group of VCFS patients. Rate of psychiatric disorders was similarly high in both groups. The familial group had fewer cardiac and palate anomalies. A significant negative correlation was found between IQ and age. Most of the adults with familial VCFS were neuropsychiatrically disabled. Thus, although familial VCFS seems to be associated with a milder physical phenotype than nonfamilial VCFS, the neuropsychiatric deficits are significant in both types, at all ages.

Transcription complexes synthesizing attenuated RNA can serve as a model system for analyzing elongation factors.

In vitro transcription elongation, in HeLa whole cell extract, is partially blocked at the Ad2 and synthetic (8 Ts) attenuation sites when transcription elongation is performed at increasing KCl concentrations (0.2-0.5 M KCl) but not at the standard KCl concentration (50 mM). Furthermore, if briefly initiated transcription complexes are chromatographed on Sephacryl column at increased KCl concentration and the complexes, which are eluted in the void volume, are diluted to 50 mM KCl, they will elongate a substantial fraction of the briefly initiated nascent RNA into attenuated RNA. The addition of a crude preparation of a stimulatory factor to the complexes diluted to 50 mM KCl prevents the elongation blocks. Based on the notion that putative elongation factors dissociate from the transcription complexes at increasing KCl concentrations and in the Sephacryl column they elute after the initiation complexes, we suggest that the column-purified transcription complexes, which have been depleted of elongation factors, can serve as a model system for determining the activities of factors during elongation.

Duplicated phosphoglucose isomerase genes in avocado.

Avocado (Persea americana) cultivars were assayed for phosphoglucose isomerase (PGI) isozymes using starch gel electrophoresis. Three PGI genes were identified: one monomorphic locus, Pgi-I, coding for the plastid isozyme and two independently assorting loci, Pgi-2 and Pgi-3, coding for the cytosolic isozymes. The genetic analysis was based on comparisons of PGI zymograms from somatic and pollen tissue and on Mendelian analysis of progeny from selfed trees. The isozymic variability for PGI can be used for cultivar identification and for differentiating between hybrid and selfed progeny in avocado breeding.

Design and synthesis of bio-isosteres of thymidine triphosphate.

This paper describes the design and synthesis of potential isosteres of triphosphates which should show enhanced metabolic stability and lipophilicity compared to triphosphates. The triphosphate isosteres were then linked to nucleosides and evaluated for their inhibitory activity against HIV infection.

Quantitative vaginal microflora in women convalescent from toxic shock syndrome and in healthy controls.

We performed sequential and quantitative vaginal cultures obtained from 8 women within 4 days to 3 years (average, 15.8 months) after their recovery from classic menstrual toxic shock syndrome (TSS) and from 11 healthy women who served as age-matched controls. Apart from tampon use, which was significantly less frequent in TSS women after their acute illness, no demographic differences were observed in the two groups. Significantly lower total aerobic and anaerobic bacterial counts were found in TSS women than in healthy controls (P less than 0.05, Mann-Whitney test). These differences were most profound during the menstrual (aerobes) and premenstrual (aerobes and anaerobes) sample times, whereas no difference in bacterial counts was observed in the mid-cycle samples. Although the less frequent usage of tampons among TSS women after their acute illness might explain the lower aerobic counts in menstrual specimens, this is unlikely to explain the significantly lower aerobic and anaerobic counts observed in premenstrual samples when tampons were not used in either group. It is possible that these differences in the quantitative vaginal microflora were a direct result of recent TSS in these women. Alternatively, disruption of the normal indigenous microflora could have predisposed these women to acute TSS by alteration of the resistance of vaginal colonization to pathogenic microorganisms.

PIP: Sequential and quantitative vaginal cultures obtained from 8 women within 4 days-3 years (average, 15.8 months) after their recovery from classic menstrual toxic shock syndrome (TSS) and from 11 healthy women who served as age-matched controls were performed. Apart from tampon use, which was significantly less frequent in TSS women after their acute illness, no demographic differences were observed in the 2 groups. Significantly lower total (aerobic and anaerobic bacterial counts were found in TSS women than in healthy controls (P0.05, Mann-Whitney test). These differences were most profound during the menstrual (aerobes) and premenstrual (aeobes and anaerobes) sample times, whereas no difference in bacterial counts was observed in the midcycle samples. Although the less frequent usage of tampons among TSS women after their acute illness might explain the lower aerobic counts in menstrual specimens, this is unlikely to explain the significantly lower aerobic and anaerobic counts observed in premenstrual samples when tampons were not used in either group. It is possible that these differences in the quantitative vaginal microflora were a direct result of recent TSS in these women. Alternatively, disruption of the normal indigenous microflora could have predisposed these women to acute TSS by alteration of the resistance of vaginal colonization to pathogenic microorganisms.

Specific interaction between the nonphosphorylated form of RNA polymerase II and the TATA-binding protein.

Fractionation of a transcription-competent HeLa cell extract on a column containing one copy of the heptamer repeat (YSPTSPS) present in the carboxy-terminal domain (CTD) of the largest subunit of RNA polymerase II resulted in the loss of transcriptional activity. Fractionation of the extracts on columns containing mutations of the heptamer repeat was without effect. Such transcriptionally inactive extracts regained their ability to specifically transcribe different class II promoters upon the addition of human TFIID, recombinant yeast TATA-binding protein (TBP), or proteins bound to the column. Fractionation of RNA polymerase II on columns containing human or yeast TBP resulted in the specific retention of the nonphosphorylated form of RNA polymerase II. The phosphorylated form of the enzyme was unable to interact with TBP. The specific interaction of RNA polymerase II with TBP was mediated by the CTD of RNA polymerase II.