Biomedical subjects

R Rothstein

Publications and source records attributed to R Rothstein.

At least 37 records · Page 2Linked to original sources

PubMed1999

The colonoscopic miss rate and true one-year recurrence of colorectal neoplastic polyps. Polyp Prevention Study Group.

OBJECTIVE: Studies of tandem colonoscopies have reported that 15-25% of neoplastic polyps <1 cm in size and 0-6% of larger polyps are overlooked at the time of colonoscopy. We determined the miss rate and "true" 1-yr recurrence of neoplastic polyps in a population of patients reflecting a broad spectrum of different gastroenterology practice settings. METHODS: Patient data from several sources were examined for repeat colonoscopies performed on the same patient within 120 days of each other. Examination pairs were included for analysis if both colonoscopies had good preps and reached the cecum. The miss rate was calculated by two methods: 1) a pooled rate, the total number of polyps on all second examinations divided by the total number on both examinations, and 2) a within-person rate, the average of the individual miss-rates. We estimated a "true" 1-yr recurrence rate by subtracting the proportion of patients with a missed neoplastic polyp from the proportion of patients with a neoplastic polyp found at 1 yr. RESULTS: A total of 76 colonoscopy pairs a mean 47 days apart (range, 1-119 days) were identified from a total of approximately 15,000 examinations and used to calculate the overall miss rates. For the category "all polyps" (neoplastic and nonneoplastic polyps), 17% by the pooled method and 11% by the within-person method were missed. The corresponding rates for neoplastic polyps were 12% by the pooled method and 8% by the within-person method. A total of 17% of patients had one or more neoplastic polyps missed on the initial examination. The observed 1-yr recurrence rate was determined from 1,314 colonoscopy pairs performed a mean of 379 days apart and found to be 28% for neoplastic polyps. By comparing this to the proportion of patients with one or more missed neoplastic polyps, we found the true 1-yr recurrence of neoplastic polyps to be 11%. CONCLUSION: There is a significant colonoscopic miss rate for neoplastic polyps and "all polyps" in clinical practice that is comparable to that previously stated in special research settings. The within-person rate more accurately reflects the true colorectal polyp miss rate for any given colonoscopic exam than does the pooled rate. The difference between the observed 1-yr recurrence rate and the proportion of patients with a missed polyp represents the true 1-yr recurrence of neoplastic polyps.

Adenomatous Polyps↗

PubMed1999

Calcium supplements and colorectal adenomas. Polyp Prevention Study Group.

Experimental and observational findings suggest that calcium intake may protect against colorectal neoplasia. To investigate this hypothesis, we conducted a randomized, double-blind trial of colorectal adenoma recurrence. Nine hundred thirty patients with a recent history of colorectal adenomas were randomly given calcium carbonate (3 gm daily; 1200 mg elemental calcium) or placebo, with follow-up colonoscopies one and four years after the qualifying examination. The main analysis focused on new adenomas found after the first follow-up endoscopy, up to (and including) the second follow-up examination. Risk ratios of at least one recurrent adenoma and ratios of the average numbers of adenomas were calculated as measures of calcium effect. There was a lower risk of recurrent adenomas in subjects assigned calcium. Eight hundred thirty-two patients had two follow-up examinations and were included in the main analysis; the adjusted risk ratio of one or more adenomas was 0.81 (95% CI 0.67 to 0.99); the adjusted ratio of the average numbers of adenomas was 0.76 (95% CI 0.60 to 0.96). Among subjects who had at least one follow-up colonoscopy, the adjusted risk ratio of one or more recurrent adenomas was 0.85 (95% CI 0.74 to 0.98). The effect of calcium seemed independent of initial dietary fat and calcium intake. No toxicity was associated with supplementation. These findings indicate that calcium supplementation has a modest protective effect against colorectal adenomas, precursors of most colorectal cancers.

Adenoma↗

PubMed1998

Safety profiles of leading nonsteroidal anti-inflammatory drugs.

Recently introduced nonsteroidal anti-inflammatory drugs (NSAIDs) have capitalized on new formulations or unique physical and pharmacologic properties in an attempt to provide a greater margin of gastrointestinal (GI) safety. The use of enteric coatings and nonoral or pro-drug formulations have not necessarily provided the expected safety, but other properties have been identified that appear to be more promising. However, as demonstrated by oxaprozin, considered to be one of the least safe NSAIDs but one of the leading drugs on the US market, success may not be dependent on safety. In contrast, the improved tolerability of 2 other new NSAIDs, nabumetone and etodolac, has been established in clinical trials and limited postmarketing surveillance. This improved tolerability is probably associated with several pharmacologic properties that have been suggested to contribute to GI safety: (1) nonacidic pro-drug formulation; (2) lack of enterohepatic recirculation; (3) a short plasma half-life; and (4) preferential inhibition of cyclo-oxygenase-2 (COX-2). Although these factors may not improve efficacy, their incorporation into the design of drugs suggests that safer NSAIDs may be a clinical reality. However, the safety and clinical value of any new drug for the general population will be validated only through extensive postmarketing surveillance.

Anti-Inflammatory Agents, Non-Steroidal↗

PubMed1998

High-resolution YAC-cosmid-STS map of human chromosome 13.

We have assembled a high-resolution physical map of human chromosome 13 DNA (approximately 114 Mb) from hybridization, PCR, and FISH mapping data using a specifically designed set of computer programs. Although the mapping of 13p is limited, 13q (approximately 98 Mb) is covered by an almost continuous contig of 736 YACs aligned to 597 contigs of cosmids. Of a total of 10,789 cosmids initially selected from a chromosome 13-specific cosmid library (16,896 colonies) using inter-Alu PCR probes from the YACs and probes for markers mapped to chromosome 13, 511 were assembled in contigs that were established from cross-hybridization relationships between the cosmids. The 13q YAC-cosmid map was annotated with 655 sequence tagged sites (STSs) with an average spacing of 1 STS per 150 kb. This set of STSs, each identified by a D number and cytogenetic location, includes database markers (198), expressed sequence tags (93), and STSs generated by sequencing of the ends of cosmid inserts (364). Additional annotation has been provided by positioning 197 cosmids mapped by FISH on 13q. The final (comprehensive) map, a list of STS primers, and raw data used in map assembly are available at our Web site (genome1.ccc.columbia.edu/ approximately genome/) and can serve as a resource to facilitate accurate localization of additional markers, provide substrates for sequencing, and assist in the discovery of chromosome 13 genes associated with hereditary diseases.

Animals↗

PubMed1998

A suppressor of two essential checkpoint genes identifies a novel protein that negatively affects dNTP pools.

In Saccharomyces cerevisiae, MEC1 and RAD53 are essential for cell growth and checkpoint function. Their essential role in growth can be bypassed by deletion of a novel gene, SML1, which functions after several genes whose overexpression also suppresses mec1 inviability. In addition, sml1 affects various cellular processes analogous to overproducing the large subunit of ribonucleotide reductase, RNR1. These include effects on mitochondrial biogenesis, on the DNA damage response, and on cell growth. Consistent with these observations, the levels of dNTP pools in sml1 delta strains are increased compared to wild-type. This effect is not due to an increase in RNR transcription. Finally, both in vivo and in vitro experiments show that Sml1 binds to Rnr1. We propose that Sml1 inhibits dNTP synthesis posttranslationally by binding directly to Rnr1 and that Mec1 and Rad53 are required to relieve this inhibition.

Amino Acid Sequence↗

PubMed1998

Effect of leuprolide acetate in treatment of abdominal pain and nausea in premenopausal women with functional bowel disease: a double-blind, placebo-controlled, randomized study.

We have previously reported impressive results in using a gonadotropin-releasing hormone analog, leuprolide acetate (Lupron), in the treatment of moderate to severe symptoms (especially abdominal pain and nausea) in patients with functional bowel disease (FBD). Pain is the hallmark of patients with FBD, and there is no consistent therapy for the treatment of these patients. The purpose of the present study was to expand the investigation to study similar patients (menstruating females) in a multicenter, double-blind, placebo-controlled, randomized study using Lupron Depot (which delivers a continuous dose of drug for one month), 3.75 mg (N = 32) or 7.5 mg (N = 33), or placebo (N = 35) given intramuscularly every four weeks for 16 weeks. Symptoms were assessed using daily diary cards to record abdominal pain, nausea, vomiting, early satiety, anorexia, bloating, and altered bowel habits. Additional assessment tools were quality of life questionnaires, psychological profile, oral-to-cecal transit using the hydrogen breath test, antroduodenal manometry, reproductive hormone levels, and global evaluations by both patient and investigator. Patients in both Lupron Depot-treated groups showed consistent improvement in symptoms; however, only the Lupron Depot 7.5 mg group showed a significant improvement for abdominal pain and nausea compared to placebo (P < 0.001). Patient quality of life assessments and global evaluations completed by both patient and investigators were highly significant compared to placebo (P < 0.001). All reproductive hormone levels significantly decreased for both Lupron Depot-treated groups by week 4 and were significantly different compared to placebo at week 16 (P < 0.001). This study shows that leuprolide acetate is effective in controlling the debilitating symptoms of abdominal pain and nausea in patients with FBD.

Abdominal Pain↗

PubMed1998

The development of dysplasia and adenocarcinoma during endoscopic surveillance of Barrett's esophagus.

OBJECTIVE: Periodic endoscopic surveillance is generally recommended for patients with Barrett's esophagus. The optimal follow-up strategy for uncomplicated Barrett's esophagus is controversial, in part because of limited data on the rate of neoplastic progression (through the sequence of metaplasia-dysplasia-carcinoma) during endoscopic surveillance. This study aims to quantify the development of dysplasia in patients with uncomplicated Barrett's esophagus and to explore clinical risk factors associated with the development of dysplastic lesions. METHODS: We identified 102 patients with endoscopic evidence of Barrett's esophagus and the presence of specialized columnar epithelium who had received endoscopic surveillance for adenocarcinoma at our medical center between 1970 and 1994. We abstracted endoscopic and histologic data from the medical record. All specimens that showed any degree of atypia (per report) were reexamined in blinded fashion by a team of study pathologists who indicated the grade of dysplasia. Time to first diagnosis of dysplasia was plotted using Kaplan-Meier survival curves, and risk factors for development of dysplasia were assessed using Cox regression. RESULTS: During 563 patient-yr of endoscopic follow-up, three patients developed adenocarcinoma at least 4 yr after initial diagnosis (one developed adenocarcinoma of the cardia, which was incidentally detected during surveillance for Barrett's esophagus). At some point during follow-up, 19 patients developed new onset, low grade dysplasia and four developed high grade dysplasia. None of the patients who had received antireflux surgery developed dysplasia. CONCLUSION: If confirmed by larger follow-up studies, our results suggest that surveillance endoscopy can be safely deferred for at least 2 yr following an initial biopsy that is negative or indeterminate for dysplasia. Adoption of this approach would substantially reduce the cost of surveillance for adenocarcinoma. Future trials should explore the role of antireflux surgery in protecting against neoplastic transformation of Barrett's esophagus.

Adenocarcinoma↗

PubMed1997

Holliday junctions accumulate in replication mutants via a RecA homolog-independent mechanism.

The Holliday junction recombination intermediate, an X-shaped DNA molecule (xDNA), was analyzed at rDNA in mitotically growing yeast. In wild-type cells, xDNA is only detected at S phase, suggesting that recombination is stimulated to repair replication-related lesions. A search for mutations that increase the level of xDNA uncovered a gene encoding a subunit of DNA polymerase alpha. Systematic examination of replication mutants revealed that defects in polymerase alpha and delta but not the epsilon complex stimulate the level of xDNA. These xDNAs are Holliday junctions and not replication intermediates. The level of Holliday junctions is greatly reduced in rad52 mutants, but surprisingly, not in mutants defective in the three known mitotically expressed yeast RecA homologs.

DNA Polymerase II↗

PubMed1997

The complete set of predicted genes from Saccharomyces cerevisiae in a readily usable form.

Nearly all of the open reading frames (ORFs) of the yeast Saccharomyces cerevisiae have been synthesized by PCR using a set of approximately 6000 primer pairs. Each of the forward primers has a common 22-base sequence at its 5' end, and each of the back primers has a common 20-base sequence at its 5' end. These common termini allow reamplification of the entire set of original PCR products using a single pair of longer primers-in our case, 70 bases. The resulting 70-base elements that flank each ORF can be used for rapid and efficient cloning into a linearized yeast vector that contains these same elements at its termini. This cloning by genetic recombination obviates the need for ligations or bacterial manipulations and should permit convenient global approaches to gene function that require the assay of each putative yeast gene.

DNA Primers↗

PubMed1997

Cloning-free PCR-based allele replacement methods.

Efficient homologous recombination permits the directed introduction of specific mutations into the yeast genome. Here we describe a cloning-free, PCR-based allele replacement method that simplifies allele transfer between yeast strains. The desired allele from one strain is amplified by PCR, along with a selectable/counterselectable marker. After transformation, the resident allele in the target strain is replaced by creating a duplication of the new allele. Selection for direct repeat recombinants results in a single copy of the new allele in the target strain. Specifically, the desired allele is amplified by PCR with a pair of adaptamers, which are chimeric oligonucleotides that are used to amplify the allele and differentially tag its 5' and 3' ends. These tags allow the directed fusion to two different, but overlapping, regions of an appropriately tagged selectable/counterselectable marker after a second round of PCR amplification. Following cotransformation of the two fusion fragments into yeast, homologous recombination efficiently generates a duplication of the amplified allele flanking the intact selectable marker in the genome. After counterselection, only the desired allele is retained as a result of direct repeat recombination. A simple modification of this method allows the creation of de novo mutations in the genome.

Alleles↗

PubMed1996

Direct association between the yeast Rad51 and Rad54 recombination proteins.

The RAD54 and RAD51 genes are involved in genetic recombination and double-strand break repair in the yeast Saccharomyces cerevisiae. The Rad51 protein is thought to be a yeast analogue of the Eschericia coli recA gene product and catalyzes strand exchange between homologous single- and double-stranded DNAs in vitro. RAD54 exhibits homologies to several known ATPases and is a member of the SWI2/MOT1 family. We show here that the Rad54 protein interacts with the Rad51 protein in vivo and in vitro and that the NH2-terminal 115 residues of the Rad54 protein are necessary for this interaction. Combined with previously reported results, these data imply that the Rad54 protein is part of a multiprotein yeast recombination complex.

Binding Sites↗

PubMed1996

DNA strand annealing is promoted by the yeast Rad52 protein.

The Saccharomyces cerevisiae RAD52 gene plays a pivotal role in genetic recombination. Here we demonstrate that yeast Rad52 is a DNA binding protein. To show that the interaction between Rad52 and DNA is direct and not mediated by other yeast proteins and to facilitate protein purification, a recombinant expression system was developed. The recombinant protein can bind both single- and double-stranded DNA and the addition of either Mg2+ or ATP does not enhance the binding of single-stranded DNA. Furthermore, a DNA binding domain was found in the evolutionary conserved N terminus of the protein. More importantly, we show that the protein stimulates DNA annealing even in the presence of a large excess of nonhomologous DNA. Rad52-promoted annealing follows second-order kinetics and the rate is 3500-fold faster than that of the spontaneous reaction. How this annealing activity relates to the genetic phenotype associated with rad52 mutant cells is discussed.

DNA Repair↗

PubMed1996

Sterol esterification in yeast: a two-gene process.

Unesterified sterol modulates the function of eukaryotic membranes. In human cells, sterol is esterified to a storage form by acyl-coenzyme A (CoA): cholesterol acyl transferase (ACAT). Here, two genes are identified, ARE1 and ARE2, that encode ACAT-related enzymes in yeast. The yeast enzymes are 49 percent identical to each other and exhibit 23 percent identity to human ACAT. Deletion of ARE2 reduced sterol ester levels to approximately 25 percent of normal levels, whereas disruption of ARE1 did not affect sterol ester biosynthesis. Deletion of both genes resulted in a viable cell with undetectable esterified sterol. Measurements of [14C]acetate incorporation into saponified lipids indicated down-regulation of sterol biosynthesis in the are1 are2 mutant cells. With the use of a consensus sequence to the yeast and human genes, an additional number of the ACAT gene family was identified in humans.

Acetates↗

PubMed1996

Gene conversion plays the major role in controlling the stability of large tandem repeats in yeast.

The genomic stability of the rDNA tandem array in yeast is tightly controlled to allow sequence homogenization and at the same time prevent deleterious rearrangements. In our study, we show that gene conversion, and not unequal sister chromatid exchange, is the predominant recombination mechanism regulating the expansion and contraction of the rDNA array. Furthermore, we found that RAD52, which is essential for gene conversion, is required for marker duplication stimulated in the absence of the two yeast type I topoisomerases. Our results have implications for the mechanisms regulating genomic stability of repetitive sequence families found in all eukaryotes.

Base Sequence↗

PubMed1996

A high-resolution annotated physical map of the human chromosome 13q12-13 region containing the breast cancer susceptibility locus BRCA2.

Various types of physical mapping data were assembled by developing a set of computer programs (Integrated Mapping Package) to derive a detailed, annotated map of a 4-Mb region of human chromosome 13 that includes the BRCA2 locus. The final assembly consists of a yeast artificial chromosome (YAC) contig with 42 members spanning the 13q12-13 region and aligned contigs of 399 cosmids established by cross-hybridization between the cosmids, which were selected from a chromosome 13-specific cosmid library using inter-Alu PCR probes from the YACs. The end sequences of 60 cosmids spaced nearly evenly across the map were used to generate sequence-tagged sites (STSs), which were mapped to the YACs by PCR. A contig framework was generated by STS content mapping, and the map was assembled on this scaffold. Additional annotation was provided by 72 expressed sequences and 10 genetic markers that were positioned on the map by hybridization to cosmids.

BRCA2 Protein↗

PubMed1996

Reliability of whole crypt mitotic count as a measure of cellular proliferation in rectal biopsies.

We conducted a reliability study of whole crypt mitotic count, a measure of cellular proliferation with potential use as an intermediate marker in studies of colorectal cancer risk and prevention. The study involved biopsies taken from two distinct locations at 8-10 cm from the anal verge for 20 subjects scheduled to undergo routine endoscopy. In addition to the overall count of mitoses per crypt (mitotic count), we investigated two novel measures based on the percentages of heights of mitotic cells within crypts: the mean height, and the maximum minus minimum (max - min) height of mitoses. The max - min height was positively correlated with mitotic count (r = 0.64); however, there was little correlation between mitotic count and the mean height of mitotic cells (r = 0.12). Components of variance were estimated for the three measures; for mitotic count and max - min height, the variability between persons was substantially greater than that between locations within an individual. For mean height, the between-person and between-location variabilities were roughly equal. These results suggest that whole crypt mitotic count has promise as a reliable measure of rectal cellular proliferation, but further studies will be necessary to assess the utility of this assay.

Adult↗

PubMed1995

Transfer of yeast artificial chromosomes into mammalian cells and comparative study of their integrity.

Yeast artificial chromosomes (YACs) from the CEPH MegaYAC library (Paris, France) ranging in size from 350 to 1600 kb and mapping to the q22.1 and q22.2 regions of human chromosome 21 were transferred into mammalian cells by spheroplast fusion. The integrity of the YACs from two adjacent parts of the region was compared after retrofitting and stable transfer into mammalian cells. We found that large YACs could easily be manipulated to allow transfer of the YAC material into mammalian cells and that the size of the YAC did not appear to be limiting for fusion. However, we show that there was great variability in the integrity of the YACs from the two regions, which was not related to the size of the YACs. Four YACs in region I from sequence-tagged site (STS) G51E05 up to STS LL103 showed, in general, no loss of material and correct gene transfer into mammalian cells. In contrast, the three YACs in the more centromeric region II (from STS G51B09 up to G51E05) frequently showed a loss of human material during handling, retrofitting and transfer. As a YAC from another library covering region II was also found to be unstable, we propose that the integrity of the YACs is highly dependent on the incorporated human chromosomal DNA.

Animals↗

PubMed1995

Calcium supplementation and rectal mucosal proliferation: a randomized controlled trial.

BACKGROUND: Data from studies using rodents suggest that dietary calcium inhibits bile acid-induced mucosal damage and experimental carcinogenesis in the large bowel. However, in humans, the effect of dietary calcium and calcium supplementation on proliferation and carcinogenesis in the large bowel has been unclear. PURPOSE: To assess the effect of calcium supplementation on rectal mucosal proliferation in humans, we conducted a multicenter, randomized, placebo-controlled, double-blinded trial. METHODS: Participants were part of a larger multicenter chemoprevention trial; all were at high risk for large-bowel neoplasia, with at least one large-bowel adenoma removed endoscopically within the 3 months before study entry but with no known polyps remaining. Subjects were randomly assigned to receive daily either 3000 mg of calcium carbonate (providing 1200 mg elemental calcium) or an identical-appearing placebo tablet. During a scheduled endoscopy 6-9 months after random assignment (approximately 1 year after the qualifying endoscopy), rectal mucosal samples were obtained from 333 patients (173 assigned to calcium and 160 assigned to placebo). Proliferating cell nuclear antigen (PCNA) labeling indices (LIs) were computed as the measure of proliferation in specimens from 146 patients receiving calcium and 129 patients receiving placebo. Bromodeoxyuridine (BrdU) labeling was used to measure proliferation in a smaller number of specimens (27 calcium-receiving and 31 placebo-receiving participants). For each scorable crypt having at least one labeled cell (or surrounded by crypts with at least one labeled cell), a crypt LI was calculated as the number of labeled cells divided by the total number of crypt cells. Crypt LIs were averaged to produce a participant's average LI. RESULTS: The overall unadjusted mean PCNA LIs (+/- SE) were similar in the calcium and placebo groups (3.85% +/- 0.08% versus 3.92% +/- 0.08%, respectively, P = .30). The overall unadjusted mean BrdU LIs (+/- SE) were 3.88% +/- 0.30% in the calcium group and 3.54% +/- 0.21% in the placebo group (P = .54). PCNA labeling indices in the most luminal 40% of the crypt were small but, if anything, were higher in the calcium group. There was no patient subgroup within which calcium had an antiproliferative effect; the overall findings persisted among patients with high and low calcium intake, high and low fat intake, and high and low fiber intake. CONCLUSIONS: Calcium supplementation does not decrease rectal mucosal proliferation, as measured by PCNA (and BrdU) immunohistochemistry, in patients with previous large-bowel adenomas. This study, therefore, does not provide evidence for an anticarcinogenic effect of calcium.

Adenoma↗