Yeast TAFIIS in a multisubunit complex required for activated transcription

In higher eukaryotes the RNA polymerase II transcription factor TFIID is composed of a TATA-box-binding protein (TBP) and a set of tightly bound polypeptides, designated TBP-associated factors (TAFIIS). One or more TAFIIS are coactivators that are required for activated but not basal transcription. The eukaryotic transcription machinery is highly conserved and it is therefore puzzling that TAFIIS have not been identified in yeast. Here we use TBP as a protein-affinity ligand to isolate from yeast a multisubunit complex that is required specifically for activated transcription by RNA polymerase II. Microsequence analysis and cloning of two subunits of this complex reveal that they are the homologues of known mammalian and Drosophila TAFIIS. The genes encoding these two yeast TAFIIS are essential, suggesting that activated transcription is required for viability of Saccharomyces cerevisiae.

Facilitated binding of TATA-binding protein to nucleosomal DNA

BINDING of the TATA-binding protein (TBP) to the TATA box is required for transcription from many eukaryotic promoters in gene expression. Regulation of this binding is therefore likely to be an important determinant of promoter activity. Incorporation of the TATA sequence into nucleosomes dramatically reduces transcription initiation, presumably because of stereochemical constraints on binding of general transcription factors. Biochemical and genetic studies imply that cellular factors such as yeast SWI/SNF are required for activator function and might alter chromatin structure. One step that could be regulated during the activation process is TBP binding in chromatin 12, 13. We show here that binding of TBP to the TATA sequence is severely inhibited by incorporation of this sequence into a nucleosome. Inhibition can be overcome by ATP-dependent alterations in nucleosomal DNA structure mediated by hSWI/SNF, a putative human homologue of the yeast SWI/SNF complex. Additionally, the orientation of the TATA sequence relative to the surface of the histone core affects the access of TBP. We propose that the dynamic remodelling of chromatin structure to allow TBP binding is a key step in the regulation of eukaryotic gene expression.

Nucleosome disruption and enhancement of activator binding by a human SW1/SNF complex

CHROMATIN structure can affect the transcriptional activity of eukaryotic structural genes by blocking access of sequence-specific activator proteins (activators) to their promoter-binding sites. For example, the DNA-binding domain of the yeast GAL4 protein interacts very poorly with nucleosome cores compared with naked DNA2 (and see below), and binding of other activators is even more strongly inhibited. The way in which activators bind to nucleosomal DNA is therefore a critical aspect of transcriptional activation. Genetic studies have suggested that the multi-component SWI/SNF complex of Saccharomyces cerevisiae facilitates transcription by altering the structure of the chromatin. Here we identify and partially purify a human homologue of the yeast SWI/SNF complex (hSWI/SNF complex). We show that a partially purified hSWI/SNF complex mediates the ATP-dependent disruption of a nucleosome, thereby enabling the activators, GAL4-VP16 and GAL4-AH, to bind within a nucleosome core. We conclude that the hSWI/SNF complex acts directly to reorganize chromatin structure so as to facilitate binding of transcription factors.

Alternating irradiation and chemotherapy in stage III A and B nonsmall cell lung cancer: report of a cancer and Leukemia Group B phase II study 8636

PURPOSE

A pilot trial testing the feasibility of chemotherapy and radiotherapy was done in Stage III A and B nonsmall cell lung cancer. The schedule was designed to be consistent with the laboratory model of Looney and Hopkins.

METHODS AND MATERIALS

Treatment began with thrice-per-day radiotherapy for 3 days (16.2 Gy/nine fractions), followed by chemotherapy (cis-platinum 100 mg/m2 day 10, and vinblastine 4 mg/m2 days 10 and 12). A second cycle started on day 22, a third on day 43, and a fourth on day 64. We treated three cohorts. The first cohort received three cycles of radiotherapy alone, (48.6 Gy). The second cohort received three completed cycles, and the third received three completed cycles and a fourth radiotherapy course (64.8 Gy). Patients were evaluated for toxicity, protocol compliance, response, and survival.

RESULTS

The patients in the first cohort experienced no toxicity. Fifty-six percent (56%) of the patients treated in cohort 2 experienced severe or life-threatening myelosuppression as did 82% of those in cohort 3. Nonhematologic toxicity was not severe; one case of Grade 3 esophagitis, one of reversible adult respiratory distress syndrome, and one radiation pneumonitis. We closed the trial after accrual to the third cohort because of significant myelosuppression.

CONCLUSION

This schedule is too myelosuppressive to be used without modification.

Nuclear protein CBP is a coactivator for the transcription factor CREB

The transcription factor CREB binds to a DNA element known as the cAMP-regulated enhancer (CRE). CREB is activated through phosphorylation by protein kinase A (PKA), but precisely how phosphorylation stimulates CREB function is unknown. One model is that phosphorylation may allow the recruitment of coactivators which then interact with basal transcription factors. We have previously identified a nuclear protein of M(r)265K, CBP, that binds specifically to the PKA-phosphorylated form of CREB. We have used fluorescence anisotropy measurements to define the equilibrium binding parameters of the phosphoCREB:CBP interaction and report here that CBP can activate transcription through a region in its carboxy terminus. The activation domain of CBP interacts with the basal transcription factor TFIIB through a domain that is conserved in the yeast coactivator ADA-1 (ref. 8). Consistent with its role as a coactivator, CBP augments the activity of phosphorylated CREB to activate transcription of cAMP-responsive genes.

Stopping a clinical trial early: frequentist and Bayesian approaches applied to a CALGB trial in non-small-cell lung cancer

In May 1984, the Cancer and Leukemia Group B (CALGB) opened a phase III clinical trial for patients with stage III non-small-cell lung cancer (NSCLC). The experimental design entailed randomization of 240 patients equally to one of two treatments: radiotherapy alone or chemotherapy followed by radiotherapy. The original design was a fixed sample size design with the intent to analyse the results after 190 deaths. Shortly after the trial began, it was decided to apply group sequential concepts by using a truncated O'Brien-Fleming stopping rule, implemented via a Lan-DeMets alpha-spending function. A study monitoring committee was established to review the analyses as they were produced. The study was stopped at the fifth interim analysis in May 1987 after 155 eligible patients had been entered. This paper reviews the statistical and other considerations leading to this decision and presents later follow-up information on these patients. Some Bayesian alternatives to the standard frequentist approaches are also explored and it is demonstrated how these alternatives provide a natural way to address many of the issues raised in monitoring clinical trials.

Magnetic resonance imaging of the glenoid labrum in anterior shoulder instability

Detachment of the anterior inferior labrum and inferior glenohumeral ligament complex from the glenoid is a common lesion encountered in anterior shoulder instability while other types of labral lesions are associated with symptoms that mimic instability. Accurate delineation of labral lesion is, therefore, key in managing shoulder problems. In a prospective double-blinded fashion, we compared the magnetic resonance imaging findings with those noted at surgery in 33 patients with possible anterior shoulder instability. Of 28 surgically confirmed labral lesions, 21 were detected by imaging. Sensitivity was 75%, specificity 100%, while positive and negative predictive values were 100% and 41%, respectively. Overall accuracy was 79%. Based on a literature review and our clinical experience, we developed a classification of glenoid labra according to the type and severity of the lesions. Method of treatment correlated with clinical outcome, using this system, to a statistically significant level. Unfortunately, this system enabled accurate classification with magnetic resonance imaging in only 7 of 33 (21%) labra, with the precision necessary to affect surgical planning in our series. We conclude that magnetic resonance imaging is not useful in the surgical planning for most patients with obvious anterior shoulder instability.

Trimetrexate in malignant mesothelioma: A Cancer and Leukemia Group B Phase II study

PURPOSE

Folic acid antagonists are reported to have activity against mesothelioma. The Cancer and Leukemia Group B (CALGB) undertook this phase II study of the new antifolate, trimetrexate (TMTX), to evaluate its response rate and toxicity in chemotherapy-naive patients with malignant mesothelioma.

PATIENTS AND METHODS

Fifty-two patients were accrued to this protocol. Because of concerns about TMTX toxicity in patients with malignant effusions and/or hypoalbuminemia, the first 17 patients were treated at a dose of 6 mg/m2 daily for 5 days every 21 days. Because minimal toxicity was observed, the subsequent 35 patients were treated at a dose of 10 mg/m2.

RESULTS

Two of 17 patients (12%) in the 6-mg/m2 treatment group had a partial response (PR) and four of 34 eligible patients (12%) in the 10-mg/m2 treatment group had a PR or regression (R) of assessable disease. No patient achieved a complete response (CR). Median survival durations were 5.0 and 8.9 months in the 6- and 10-mg/m2 treatment groups, respectively, while the 2-year survival rates were identical at 18%. At the 10-mg/m2 dose, toxicity was tolerable, with one toxic death from sepsis and a 12% rate of grade 4 thrombocytopenia and granulocytopenia.

CONCLUSION

In this large trial, TMTX showed minor activity in the treatment of malignant mesothelioma. Myelosuppression was mild and dose-related. Future studies of higher doses of TMTX should be considered.

Nonoperative management of non-small cell lung cancer: the current cancer and leukemia group B experience

The Cancer and Leukemia Group B (CALGB) is studying nonoperative management in two subgroups of patients with advanced non-small cell lung cancer. In patients with regional disease, primarily those with bulky N2 or T4 disease or those with contralateral mediastinal involvement (N3), a phase III trial is under way to explore concurrent carboplatin as intensification of local therapy and additional systemic treatment. This builds on prior CALGB work demonstrating the benefits of induction chemotherapy prior to radiation for selected patients with stage III disease. For patients with still more advanced disease, a trial evaluating efficacy and cost of two supportive care modalities during intensive chemotherapy is about to begin accrual. Following its completion, the CALGB plans to evaluate new chemotherapy combinations based on one or more of the exciting new agents now being tested for the nonoperative management of non-small cell lung cancer.

Cisplatin, vinblastine, and hydrazine sulfate in advanced, non-small-cell lung cancer: a randomized placebo-controlled, double-blind phase III study of the Cancer and Leukemia Group B

PURPOSE

To assess the chemotherapy regimen of cisplatin, vinblastine, and hydrazine sulfate administered to patients with non-small-cell lung cancer (NSCLC) in a randomized, placebo-controlled double-blind phase III study.

PATIENTS AND METHODS

Between July 25, 1989 and February 1, 1991, 291 patients with stage IIIB or IV NSCLC and performance status 0 or 1 were randomized to receive cisplatin 100 mg/m2 intravenously (IV) every 28 days, vinblastine 5 mg/m2 IV per week times five, then every 2 weeks; and either hydrazine sulfate 60 mg three times per day orally or placebo. The concurrent use of corticosteroids, medroxyprogesterone, or other appetite stimulants was not permitted. Treatment groups were comparable for known prognostic variables. The primary end point of this study was survival; however, the influence of hydrazine sulfate on nutritional status, performance status, and quality of life was also assessed.

RESULTS

Analysis of 266 eligible patients showed a median survival duration of 7.78 months for the hydrazine sulfate-treated group compared with 7.70 months for the placebo-treated group (P = .65, log-rank). Objective response rates were similar for the two groups, with 4% complete responses, 20% partial responses, and 2% regressions in those treated with hydrazine sulfate; 3% complete responses, 23% partial responses, and 2% regressions in those who received placebo. The major toxicity was severe or life-threatening neutropenia, which occurred in 65% of hydrazine sulfate patients and 63% of placebo patients. There were no differences noted between the two groups in degree of anorexia, weight gain or loss, or overall nutritional status. Sensory and motor neuropathy occurred significantly more often in patients treated with hydrazine sulfate. Quality of life was significantly worse in patients who received hydrazine sulfate.

CONCLUSION

This study suggests no benefit from the addition of hydrazine sulfate to an effective cytotoxic regimen.

DNA-binding domains: targets for viral and cellular regulators

Specific DNA binding by eukaryotic transcription factors is conferred by several types of sequence motif. These domains have been extensively studied with regard to their precise interaction with DNA and the basis of sequence specificity. Evidence is accumulating that DNA-binding domains serve functions in addition to binding DNA: they are also targets of viral and cellular regulatory proteins.

Multimodality therapy for non-small-cell lung cancer

The optimal treatment strategy for patients with locally advanced (stage III) non-small-cell lung cancer remains controversial. Primary surgical resection or conventional thoracic irradiation alone results in poor long-term survival for the majority of stage III patients. Several multimodality strategies are reviewed in this article. Radiation followed by surgery may increase resectability, but its effects on survival are unproven. Sequential chemotherapy and radiation have demonstrated a survival advantage for selected stage III patients. Chemotherapy followed by surgery has also shown encouraging results, and additional studies are in progress. Concurrent chemoradiotherapy has shown conflicting results in a few randomized studies. Concurrent chemotherapy and radiation followed by surgery has been tested only in phase II trials and awaits further studies.

Promoter targeting by adenovirus E1a through interaction with different cellular DNA-binding domains

A puzzling property of the transcriptional activators encoded by several animal viruses is their ability to function promiscuously. The adenovirus E1a protein, for example, stimulates transcription of adenoviral genes as well as a wide variety of other viral and cellular genes. We show that E1a can interact with several classes of cellular DNA-binding domains and thereby be recruited to diverse promoters. Our results explain how a single protein can regulate transcription of multiple genes that lack a common promoter element.

A phase II study of recombinant beta-interferon at maximum tolerated dose in patients with advanced non-small cell lung cancer: a cancer and leukemia group B study

Forty-one patients with advanced non-small cell lung cancer (NSCLC) were entered into a phase II study of high dose recombinant interferon (rIFN)-beta. Patients received intravenous (i.v.) rIFN-beta on a Monday, Wednesday, Friday schedule with a weekly dose escalation until > or = grade 3 toxicity or 720 x 10(6) IU/dose was achieved. Thirty-eight patients were eligible. Seventeen patients received the highest planned dose of rIFN-beta and 11 experienced dose-limiting toxicity at lower doses. Ten patients developed progressive disease before grade 3 toxicity was reached. There were no objective responses observed. Significant and dose-limiting toxicities included nausea and vomiting, fever, rigors, severe dyspnea, hypotension, and hypertension. IFN-beta has no measurable antitumor activity against NSCLC even at maximum tolerated doses (MTDs).

Modeling eukaryotic transcriptional activation

In recent years, many components involved in promoter-specific transcriptional activation in eukaryotes have been identified and characterized. We argue that a proper understanding of transcriptional activation will require quantitative modeling and we outline some of the considerations that such modeling will need to take into account.

Does adjuvant chemotherapy decrease distant metastasis formation in patients with non-small cell lung cancer?

Disseminated micrometastatic disease limits the effectiveness of even the most aggressive locoregional treatment strategies in patients with early stage non-small cell lung cancer. One trial of the Lung Cancer Study Group (LCSG) demonstrated a significant decrease in the hazard rate for distant recurrence produced by adjuvant CAP chemotherapy after surgical resection and radiation therapy. French investigators found a significant decrease in distant metastases formation following sequential chemotherapy, radiation, and then additional chemotherapy compared to radiation alone in patients with stage III disease. However, other completed trials are either inconclusive, incompletely analyzed thus far or show no evidence of an effect of adjuvant chemotherapy on distant metastases. Additional data from recently completed or current trials will hopefully clarify the impact of adjuvant chemotherapy on distant micrometastases in patients with potentially curable non-small cell lung cancer (NSCLC).

Prognosis in cystic fibrosis treated with continuous flucloxacillin from the neonatal period

All newborn infants in East Anglia are screened for cystic fibrosis by blood immunoreactive trypsin assay at 7 days. Thirty eight infants with cystic fibrosis were randomised to treatment with either continuous oral flucloxacillin 250 mg/day (group P, n = 18) or with episodic antimicrobials as clinically indicated (group E, n = 20). Their progress was monitored from diagnosis to 24 months by a nurse coordinator who visited all infants regularly, at home and in hospital, to collect anthropometric, dietary, clinical, and microbiological data. Mean (range) age of confirmation of diagnosis was 5.7 weeks (1-14 weeks). There was no significant difference in birth weight, genotype, immunoreactive trypsin concentration, neonatal history, symptoms at diagnosis, pancreatic enzyme supplementation, or parental smoking history between the groups. Infants in group E had more frequent cough and a greater number of Staphylococcus aureus isolates than infants in group P. More infants of group E were admitted to hospital, had higher admission rates during the second year (19 v 5), for longer periods (6.4 v 2.2 days), despite receiving more than double the number of courses of antibiotics than group P infants (in addition to flucloxacillin). Continuous prophylactic flucloxacillin from early diagnosis of cystic fibrosis is associated with improved clinical progress during the first two years of life.

Human transcription factor YY1 represses human immunodeficiency virus type 1 transcription and virion production

The transcriptional activity of human immunodeficiency virus type 1 (HIV-1) is affected by many cellular factors. Homologies near the HIV-1 initiator region to the DNA-binding sequences of YY1, a multifunctional transcription factor known to regulate diverse viral and cellular promoters, suggested that YY1 might regulate HIV-1. Antibody to YY1 blocked the formation of complexes by HeLa cell nuclear extract and a DNA oligonucleotide encoding the HIV-1 initiator region. HIV-1 long terminal repeat (LTR) expression, as measured the expression of a transfected LTR-CAT reporter gene, was repressed more than 12-fold by the cotransfection of a YY1 expression vector. HIV-1 production by both COS-1 and CEM cells after transfection of an infectious molecular HIV-1 clone was repressed 7- to 20-fold by cotransfection of a YY1 expression vector. HIV-1 production was also decreased threefold in a CD4-positive lymphocyte cell line chronically infected with HIV-1 (8E5) after transfection of YY1. In situ hybridization studies confirmed that YY1 reduced HIV-1 RNA expression. YY1 may play an important role in the regulation of HIV-1 LTR expression in vivo and virus production by infected cells.

Phase II trial of gemcitabine (2,2'-difluorodeoxycytidine) in patients with adenocarcinoma of the pancreas

Gemcitabine is a novel nucleoside analog which demonstrated a broad spectrum of preclinical activity in solid tumor models, and responses in patients with pancreas cancer during phase I evaluation. Patients with measurable adenocarcinoma of the pancreas who had received no previous chemotherapy were eligible for this multicenter phase II clinical trial. Gemcitabine 800 mg/m2 was administered intravenously weekly for 3 consecutive weeks, followed by one week rest, every 4 weeks. Forty-four patients entered the trial; 35 had at least 2 cycles of therapy. Partial response was observed in 5 patients (11%, estimated 95% confidence interval 2-20%), with a median duration of 13 months. All responding patients had stabilization or improvement in performance status. Fourteen patients had stable disease of 4 or more months. The median WBC nadir was 3.8 x 10(3)/microliters (range 1.6-9.3) and the median absolute neutrophil (ANC) nadir was 2.0 x 10(3)/microliters (range 0.4-7.2). Thrombocytopenia - 100.0 x 10(3)/microliters was observed in 15 patients; the median platelet nadir was 123.0 (range 30.0-245.0). All patients experienced a mild to moderate flu-like syndrome. In addition, one patient had a mild hemolytic-uremic syndrome which appeared related to gemcitabine therapy. Gemicitabine demonstrated marginal activity in this resistant neoplasm, without excessive toxicity. Further evaluation, including the use of more intense dosing and/or combination therapy, is warranted.

Quality of life in patients with limited small-cell carcinoma of the lung receiving chemotherapy with or without radiation therapy, for cancer and leukemia group B

Quality of life was assessed in 57 patients with limited small-cell carcinoma of the lung utilizing psychological scales that measured mood, functional status, and cognitive impairment. These patients received chemotherapy with or without radiotherapy to the primary tumor. All patients received prophylactic cranial radiation. Patients who received the combination of chemotherapy and radiotherapy to both the primary tumor and CNS had an increase in overall survival. However, because of the increased toxicity experienced by these patients, a decrease in quality of life was documented by measures of psychological distress when compared to patients receiving chemotherapy alone. The findings support the importance of utilizing quality of life measures in addition to measures of physical toxicity so that patients can make an informed choice regarding treatment options.

A feasibility study of extended chemotherapy for locally advanced non-small cell lung cancer: a phase II trial of cancer and leukemia group B

The purpose of this study was to determine the feasibility of additional chemotherapy beyond 5 weeks of vinblastine-cisplatin followed by radiation therapy for patients with stage III non-small cell lung cancer. In this randomized phase II trial, the goal was to determine, in a similar population of patients, the toxicity of either of two additional chemotherapy programs. Ninety-one patients with stage III non-small cell lung cancer received the same induction regime of vinblastine/cisplatin/radiotherapy. In patients randomized to regime 1, an additional four cycles of vinblastine/cisplatin were given after the radiotherapy. In regimen 2, six weekly doses of carboplatin were given concurrent with the radiotherapy. The additional four cycles of vinblastine and cisplatin were completed by 34% of patients; the concurrent carboplatin program was completed by 70% of patients. Grade 3 or 4 granulocytopenia occurred in 53% of patients on regime 1 versus 17% on regime 2 (p < 0.003); grade 3 or 4 nausea/vomiting occurred in 20% of those on regime 1 versus 7% on regimen 2 (p = 0.175). Response rates and survival were similar for the two regimens, with approximately 30% of patients surviving at 2 years. Given the reduced toxicity and the improved capacity to complete the planned therapy with the concurrent carboplatin treatment, this regimen will be further examined in a phase III trial.