Cytological diagnosis of genital ureaplasma urealyticum and its importance in cervical inflammation

OBJECTIVE

Cervical smear cytology, which is a gynecological cervical cancer screening test, can provide information about the presence of pathogenic microorganisms or the inflammation they cause. Among them, Ureaplasma urealyticum (Uu), which is a subspecies of Mycoplasma was held responsible for high-grade cervical intraepithelial lesions and malignancy due to long-lasting complicated vulvovaginitis clinic. We aimed at investigating the role of Uu in the inflammatory process of the cervix and to describe the cytological features that enable it to be recognized microscopically in cervical smear test.

PATIENTS AND METHODS

Cervical smear and mycoplasma culture data of 123 women with complicated vulvovaginitis findings were evaluated. According to the Uu culture results, women were divided into two groups: the Uu-positive (n=59) and the Uu-negative group (n=64). The groups were compared in terms of cervical smear results, macroscopic view of the cervix, and secondary cytological evaluation results.

RESULTS

The presence of inflammatory signs (83.1%) in the Uu-positive group was observed to be 83.1%, whereas 67.2% in the Uu-negative group, and the difference between the two groups was found to be significant (p=0.04). Besides, the difference in aggregated polymorphonuclear leukocytes (PMNL) between Uu-positive group (59.3%) and Uu-negative group (40.6%) was statistically significant (p=0.04). Similarly, nuclear atypia of epithelial cells in the Uu-positive group (33.9%) was observed to be higher than in the Uu-negative group (17.2%) (p=0.03).

CONCLUSIONS

Uu causes inflammation of the cervix and cervical intraepithelial lesions. Aggregated PMNL observed in cervical smear cytology may be one of the findings that will give clues for Uu.

The effect of growth hormone addition protocols to poor ovarian responders in in vitro fertilization cycles

OBJECTIVE

In vitro fertilization failure (IVF) is high in women with poor ovarian response or non-responder. For this reason, the addition of adjuvant treatments to IVF protocols has come to the fore. We assessed to investigate the effects of adjuvant GH therapy initiated in the mid-luteal phase on IVF success in poor ovarian response or non-responder women.

PATIENTS AND METHODS

A retrospective study was performed in 93 poor ovarian response or non-responder women from a single center. GH treatment was added (GH-plus group) in the mid-luteal phase of the previous menstrual cycle to 47 of the women who underwent controlled ovarian stimulation with the flexible antagonist protocol. 46 women, as another group, were applied to a flexible antagonist-only protocol (GH-free group). The IVF outcome results were evaluated and compared within the groups.

RESULTS

The number of retrieved oocytes was statistically significantly higher in the GH-plus group (2.28±1.975) than in the GH-free group (1.24±1.728) (p=0.01). Although statistically insignificant (p=0.55), the clinical pregnancy rate was higher in the GH-plus group [(8/47), 17%] than in the GH-free group [(5/46, 11%]. The cancellation rate was statistically significantly higher in the GH-free group (65.2%) than in the GH-plus group (44.7%) (p=0.04). No oocyte retrieved cycle rate was higher in the GH-free group (56%) than in the GH-plus group (25%) (p=0.002).

CONCLUSIONS

Adjuvant GH therapy administration to IVF protocol in the mid-luteal phase gives poor ovarian response or non-responder women a chance to have a baby.

Abstract P5-12-09: A novel commercial LC-MS/MS assay for tamoxifen (TAM) and its major metabolites

The standard of care for women presenting with early stage- ER-positive breast cancer (BC) following "curative" surgery has been 5 years of TAM. Adjuvant treatment with TAM has changed the natural history of BC, producing a significant reduction in 5- and 10-year recurrence rates; however, because of its adverse effects, many women (approx. 40%) do not complete the recommended 5 years of treatment. Furthermore, since TAM is a pro-drug that needs to be converted to endoxifen to be effective, inter-individual variability in endogenous enzymatic activity (i.e., CYP2D6) can affect endoxifen exposure. Certain drugs (e.g., SSRIs) can also reduce endoxifen exposure by inhibiting CYP2D6.

It is thought that a reduction in endoxifen exposure reduces the efficacy of TAM treatment and increases recurrence risk. However, several recent studies contradict this hypothesis and suggest that a) there is more than one pathway to get to endoxifen, even in the presence of variant CYP2D6; and b) TAM may act through its other metabolites as well, not just endoxifen.

Thus, a CYP2D6 genetic test may overly simplify our understanding of TAM metabolism and prompt clinicians to draw the wrong conclusions. As such, it would seem useful to develop an assay to directly measure each patient's unique serum metabolite levels. The ability to quantitate all the major TAM metabolites would also allow researchers to assess which metabolite level(s) most closely correlates with both recurrence and toxicity, allowing individualized patient dosing. In this regard, results from the BIG1-98 study suggest that some metabolites may be more closely associated with adverse effects than others. This finding could be clinically useful when combined with outcomes data, as poor adherence to TAM may be an unrecognized reason for a number of recurrences that could potentially be avoided by therapeutic drug monitoring (TDM) using a sensitive and specific assay.

With this in mind we developed an HPLC-MS/MS method that quantitatively measures TAM and 6 of its major metabolites in a single assay. This high-throughput assay has been validated to CLIA '88 standards and is run in a high-volume commercial CLIA certified laboratory. Although some of the metabolites had been measured previously by HPLC or LC-MS/MS, this is the first assay that measures all of the major metabolites, including the newly identified norendoxifen.

Results

Serum from 100 women taking TAM at 20 mg/d for > 6 months was tested using this assay, and observed ranges were calculated for this patient cohort. The observed ranges from the analysis are shown in Table 1, along with the lower limit of quantitation (LLOQ) for each analyte.

Table 1. Observed ranges and LLOQs for Tamoxifen and MetaboliteAnalyteLLOQ (ng/mL)Observed Range (ng/mL)Endoxifen0.40.93-43.19Tamoxifen1.512.5-233.1N-Desmethyl Tamoxifen1.53.0-374.04-Hydroxy Tamoxifen0.20.24-5.05N-Desmethyl 4'- Tamoxifen0.41.17-19.954'-Hydroxy Tamoxifen0.40.4-6.33Norendoxifen1.2<7.3

Conclusions

A novel commercial assay has been developed for TAM and its metabolites, which for the first time allows physicians to use a TDM approach for their TAM-treated patients.

Citation Format: Clarke NJ, Weber DM, Goldman SM, Morton JW, Lagier RJ, Birse CE, Bender RA, Waldman FM. A novel commercial LC-MS/MS assay for tamoxifen (TAM) and its major metabolites. [abstract]. In: Proceedings of the Thirty-Eighth Annual CTRC-AACR San Antonio Breast Cancer Symposium: 2015 Dec 8-12; San Antonio, TX. Philadelphia (PA): AACR; Cancer Res 2016;76(4 Suppl):Abstract nr P5-12-09.

Independent validation of a prognostic genomic profile (ColoPrint) for stage II colon cancer (CC) patients

358

Background: Adjuvant therapy is not routinely recommended for stage II CC patients but may be considered for high-risk patients. In this study we aim to independently validate a genomic profile that was developed to identify high-risk patients and can assist in treatment decisions.

Methods: An 18-gene profile had been developed using gene expression data from whole genome Agilent 44K oligonucleotide arrays and was validated in samples from an independent cohort of 206 CC patients and in in-silico datasets (Salazar et al. JCO 2010 in press). The profile was translated into a robust diagnostic test (ColoPrint) using customized 8-pack arrays. For this study, 233 patients who underwent curative resection (R0) for colon cancer stages II or III at the Klinikum rechts der Isar from 1987 to 2003 were selected. Fresh frozen tissues, clinical parameters and follow-up data for all patients were available. The samples were hybridized and the ColoPrint index was determined for all samples blinded from the clinical data.

Results: Patients in this study had a median age of 64 years and median follow-up of 97 months. The median number of resected lymph nodes was 21, giving an indirect measure of the quality of surgery. In the 135 stage II patients, ColoPrint identified most patients (73%) as low risk. The 5-year distant-metastasis free survival was 95% for low-risk patients and 80% for high-risk patients. In the univariate analysis, ColoPrint was the only significant parameter to predict the development of distant metastasis with a HR of 4.1 (95% CI 1.31-13.01, p=0.009). Using clinical parameters from the ASCO recommendation (T4, perforation, less than 12 LN assessed and/ or high grade) for the identification of high-risk patients was not significant (HR 2.3; 95% CI 0.68-7.53, p=0.18) and did not add power to the ColoPrint classification. These results are in good agreement with results from the first independent validation.

Conclusions: ColoPrint is able to predict the development of distant metastasis of stage II colon cancer patients and facilitates the identification of patients who may be safely managed without chemotherapy.

[Table: see text]

The PARSC trial: A prospective study for the assessment of recurrence risk in stage II colon cancer (CC) patients using ColoPrint

602

Background: Clinical trials have not yet shown convincingly if adjuvant chemotherapy is justified for stage II CC patients of whom 25% are at risk of recurrence. An 18-gene expression profile, ColoPrint, has been developed for identifying CC cancer patients more likely to develop recurrent disease and who would be candidates for adjuvant chemotherapy. The gene signature has been validated in independent cohorts of 206 CC patients and in in-silico datasets (Salazar et al, JCO in press). The profile classified 63.2% of the stage II patients (n=134) as low risk. The HR for relapse free survival (RFS) was 3.34 (p=0.017) with a 5-year RFS rate of 90.9% (95%CI, 84.0 -97.8%) for low risk patients and 73.9% (95%CI, 59.2-88.6%) for high risk patients. Moreover, the profile stratified patients independent of ASCO clinical risk factors.

Methods: A prospective trial, PARSC (Prospective Study for the Assessment of Recurrence Risk in Stage II CC Patients Using ColoPrint) has been initiated. The main objectives are: (1) determine risk assessment by ColoPrint profile versus clinical parameters based on local protocol and ASCO high-risk recommendations in stage II patients; (2) establish proportion of ′good prognosis′ and ′poor prognosis profile′ in various countries; and (3) validate the power of risk assessment and compare performance of ColoPrint and clinical risk assessment in estimating 3 year relapse rate. Inclusion criteria: age ≥ 18 years, adenocarcinoma of the colon, stage II,no neoadjuvant systemic therapy, no synchronous tumors, fresh tumor sample, and written informed consent. The treatment of the patient is at the discretion of the physician.

Results: The trial started in Sept. 2008 with currently 26 participating sites in 11 countries. So far, 223 stage II patients have been enrolled of whom 183 are eligible. 11 patients were rejected because of prior malignancies; 24 patients were rejected based on low tumor content of the sample (< 30% tumor cells), 3 patients had rectal cancer and 2 synchronous tumor.

Conclusions: The aim is to enroll 600 stage II patients to differentiate between 3 year relapse- free survival predicted by ColoPrint versus clinical factors.

[Table: see text]

Activity of Plasmid Replicons in CAULOBACTER CRESCENTUS : Rp4 and Cole1

The RP4 replicon was detected as covalently-closed circular DNA in Caulobacter crescentus strains into which it had been transferred from Escherichia coli. RP4-mediated transfer of ColE1-associated markers into C. crescentus occurred, but only as the result of transposon-mediated events. Both transposition of a ColE1-associated marker onto RP4 and cointegration of ColE1 with RP4 were observed. Chimeric plasmids containing both a ColE1 and an RP4 origin of replication were stably maintained in C. crescentus , but similar plasmids lacking the RP4 origin of replication were not stably maintained in C. crescentus. Thus we show that the ColE1 replicon cannot be maintained in C. crescentus unless it is covalently linked to another replicon, such as RK2, that can be maintained.

The 70-gene profile and chemotherapy benefit in 1,600 breast cancer patients

512

Background: The 70-gene expression profile (MammaPrint) is validated as an independent prognostic indicator for breast cancer patients with T1–2 node-negative and positive disease regardless of estrogen receptor status. Here we present the relationship between MammaPrint outcome and chemotherapy benefit in the adjuvant setting. Methods: We performed a pooled analysis of 1,637 patients with MammaPrint outcomes (T1–2, node-negative and positive invasive breast cancer and median FU 7.1 yrs) to determine the chemotherapy benefit of patients treated with adjuvant chemotherapy in addition to endocrine therapy. Patients were collected from 7 large datasets at multiple institutions across Europe. Results: In this meta-analysis, MammaPrint assigned 772 patients (47%) to “low risk” and 865 (53%) to “high risk”. In total 349 patients were treated with endocrine therapy alone, whereas 226 were treated with both chemo- and endocrine therapy. Patients with poor prognosis MammaPrint profile had a substantial benefit from chemotherapy: At 5 years, distant disease-free survival was improved from 69% to 88% (HR 0.28 (95% CI 0.14–0.56, p<0.001) when chemotherapy was added to hormonal therapy. The results remained significant in multivariate analysis including stratification by standard clinico-pathologic prognostic factors. Patients classified by MammaPrint as good prognosis (“low risk”) had no significant benefit from chemotherapy (p=0.962). Conclusions: The 70-gene MammaPrint profile is not only a strong and independent prognostic indicator for patients with early stage breast cancer, but it may also be predictive for the benefit of chemotherapy. While MammaPrint “high risk” classified patients demonstrate a clear benefit from adjuvant chemotherapy added to hormonal therapy, patients classified by MammaPrint as “low risk” for recurrence do not appear to benefit from the addition of chemotherapy to hormonal treatment alone.

[Table: see text]

Outcome prediction by the 70-gene profile in the context of the National Comprehensive Cancer Network (NCCN) guidelines

535

Background: According to the NCCN consensus guidelines molecular profiling for breast cancer prognosis may be used in patients with ER-positive, Her2-negative and LN-negative disease. Current proposed NCCN clinical risk assessment suggests adjuvant treatment for the majority of these patients. The 70-gene profile (MammaPrint) is validated as an independent prognostic indicator for patients with lymph node-negative and positive disease. Prognosis prediction by MammaPrint may be more suitable to indicate who needs adjuvant chemotherapy in addition to endocrine therapy. Methods: 566 tumor samples of women with ER-positive, Her2-negative and LN- negative breast cancer from 5 previously reported studies were analyzed and classified by MammaPrint as good or poor prognosis. 10-year breast cancer-specific survival (BCSS) was analyzed according to MammaPrint and the NCCN guidelines. Results: Median follow-up was 3.5 years (range 0.1–21.1). 380 of 566 patients (67%) were classified as good and 186 (33%) as poor prognosis by MammaPrint. Using the NCCN guidelines, 7% were classified as low and 93% as high risk respectively. 349 patients (62%) received no adjuvant treatment, 17% received hormonal treatment only, 2% chemotherapy only and 20% both respectively. At 10 years, BCSS was 91% vs. 67% for the good and poor prognosis groups (HR 4.0 [95%CI 2.0–7.9], p<0.001) whith MammaPrint risk assessment. If the NCCN guidelines were used, BCSS was 86% vs. 83% for the low and high risk groups (HR 1.11 [0.3–4.6), p=0.888). In multivariate analysis, adjusted for known prognostic factors and adjuvant therapy, only MammaPrint and histological grade were independent predictors for 10-year-BCSS with HRs of 2.8 (1.3–6.1, p=0.008) and 1.9 (1.1–3.1, p=0.015), respectively. Conclusions: MammaPrint is a strong and independent prognostic indicator in ER-positive, Her2-negative, LN-negative breast cancer and is discordant in 62% of cases when compared with the NCCN guidelines. MammaPrint identifies approximately 66% of NCCN high risk patients as having a good prognosis. Integration of MammaPrint into clinical risk assessment and adjuvant treatment selection can provide a large benefit for management of patients with endocrine-responsive early breast cancer.

[Table: see text]

Combining multigene profiling of molecular subtypes with the 70-gene profile for classification of breast cancer

11083

Background: Classification of breast cancers into molecular subtypes may be important for accurate selection of therapy for patients. Herein we report a multigene profile for classification of breast cancer into molecular subtypes. The profile separates tumors into hormone receptor (HR)+/luminal-like, HER2+/ERBB2-like, and triple negative/basal-like subclasses. Methods: A multi-gene profile was developed based on a series of 200 tumor samples of known ER, PR and HER2 receptor status (concordant IHC and gene expression result) hybridized on 44k microarrays. The profile classifies 96% concordant to the molecular subtypes named luminal-, ERBB2- or basal-type as published by Perou et al (Perou et al, Nature, 2000; Fan et al, NEJM, 2005). The profile was validated using 469 independent samples as well as on two publically available gene expression datasets (n=251 and n=159). Results: The profile classified 66% (712) as luminal-like, 18% (194) ERBB2-like, and 16% (173) as basal-like. As compared to single-marker readout for the presence of ER, PR and HER2, 13% of the samples that were scored positive for presence of ER/PR did not express a luminal-like gene profile. Samples with a ERBB2-like or basal-like gene profile showed equally poor 5-year survival rates of ∼65%. However, the ERBB2-like subset of MammaPrint low risk patients (15%) showed an 89% (95%CI, 71–100) survival rate without trastuzumab treatment. When the luminal-like subtype was separated into “high-” and “low-risk” by MammaPrint the survival rate was 56% (95%CI, 46–68) for high-risk luminal-like samples and 94% (95%CI, 90–99) for low-risk samples. Conclusions: The developed multigene profile can classify breast tumors into luminal-, ERBB2- and basal-like subgroups. By combining this molecular subtyping with MammaPrint risk-classification specific groups of patients can be recognized that that are at high risk of recurrence. The low risk patients within the luminal- and ERBB2-like subclasses have a very low risk of recurrence. Implementation of this knowledge can improve the clinical management of breast cancer patients.

[Table: see text]

A sensitive method for detection of EGFR gene mutations in plasma

18027

Background: Somatic mutations in the tyrosine kinase (TK) domain of the EGFR gene are associated with clinical response to TK inhibitors in patients with non-small cell lung cancer. An assay that detects such mutations in the plasma would provide a noninvasive technique to assess suitability for TK inhibitor therapy. Here we describe: 1) the development of a sensitive assay to detect the E746-A750 deletion in the TK domain of EGFR in plasma; and 2) optimization of the method for plasma DNA extraction. Methods: Our assay uses Mse I to specifically digest wild-type (WT) genomic DNA (gDNA) to reduce non-specific amplification. After digestion, samples are PCR- amplified using 1 unlabeled primer and 1 FAM-labeled primer spanning the E746-A750 deletion region and fluorescence detected with an automated analyzer. Serial dilution studies were conducted using H1650 gDNA (del E746-A750 cell line) diluted in WT gDNA after Mse I digestion. To assess detection of the deletion in plasma, 3–4 mL whole blood was spiked with 1–37 ng H1650 gDNA; gDNA from the separated plasma was then extracted (silica column/2-propanol precipitation), digested with Mse I, and amplified as above. Several extraction methods were evaluated using pooled plasma samples and PBS spiked with 10–350 ng gDNA: silica column, magnetic bead, phenol:chloroform, and 2-propanol precipitation. Results: Digestion of the WT EGFR allele followed by deletion-specific fluorescent PCR allowed detection of caof ca. 1 copy of the del E746-A750 EGFR gene (10 pg gDNA) diluted to 0.001%. Furthermore, del E746-A750 was successfully detected in 1/5 the final DNA volume (5 μl) in all spiked blood samples. Magnetic bead-based DNA extraction yielded the highest percent recovery of gDNA from PBS (69% recovery of the 10-ng sample). Phenol:chloroform extraction gave the highest yield with pooled plasma samples. Conclusions: The combination of an optimized DNA extraction method, clearing the plasma DNA sample of amplifiable WT DNA by restriction digestion, and mutation-specific fluorescent PCR provides a highly sensitive assay for detection of somatic mutations in plasma.

No significant financial relationships to disclose.

Preliminary study of three tumor markers for hepatocellular carcinoma: AFP, AFP-L3, and Glypican-3

15014

Background: a-Fetoprotein (AFP) is the most widely used biochemical marker for detection of hepatocellular cancer (HCC). AFP is also elevated in acute and chronic liver disease, limiting its utility as an early indicator of HCC. Recently, AFP-L3 and glypican 3 (GPC3) have been reported for early detection of HCC. AFP-L3 is a glycoform of AFP produced by malignant liver cells. Measurement of AFP-L3 as a percentage of total AFP helps distinguish non-malignant hepatic disease from HCC. GPC3 is a heparin sulfate proteoglycan anchored to the plasma membrane. The level of GPC3 in the serum of HCC patients is higher than in the serum of healthy adults or patients with non-malignant hepatopathy. We tested the concordance of AFP, AFP, AFP-L3%, and GPC3and GPC3 to determine if their simultaneous measurement may increase the sensitivity of identifying individuals at risk for HCC. Method: De-identified clinical samples (n = 176) submitted for AFP-L3% measurement were tested. AFP and AFP-L3 levels were measured using the LiBASys automated analyzer (Wako Chemicals USA Inc, Richmond, VA). GPC3 levels were measured with a commercial ELISA kit (BioMosaics, Inc, Burlington, VT). To assess concordance we categorized results according to accepted cut-off values for AFP and AFP-L3, and a clinically established reference range for GPC3. Results: Fourteen of the 176 samples had elevated GPC3 (=180pg/mL), 6 (43%) of which had normal AFP values (<20ng/mL). Forty- seven of the 176 samples had elevated AFP-L3% (L3 =10%), 6 (12.8%) of which had normal AFP levels. Conclusion: These data suggest that GPC3 and AFP-L3% may be used as supplemental markers, and the simultaneous determination of AFP, AFP-L3, and GPC3 may provide a higher sensitivity for identifying individuals with increased risk of HCC.

[Table: see text]

No significant financial relationships to disclose.

Clinical validation of a self-organizing map (SOM)-based quantitative prediction algorithm to determine the site of origin of cancers of unknown primary (CUP)

21064

Background: As many as 100,000 new cases of CUP are diagnosed each year in the United States. Identifying the site of origin of the CUP is critical for effective cancer management, and several genomic assays have been developed to facilitate this process. The genomic profile generated does not always fit into a discrete classification, however, and communicating results in a simple, easily understood format is important to clinical practice. Methods: We created a novel algorithm that combines SOMs for qualitative visualization with a quantitative clustering algorithm to predict the site of origin of metastatic cancers. We trained the algorithm on a dataset of 231 tumor-bank samples from 9 primary sites. After fixing all thresholds and algorithm settings, we evaluated the algorithm's performance in making a correct first or second prediction on a second blinded and independent dataset of 63 samples. Results: The algorithm correctly predicted the primary site in 82% of cases with the first prediction, and 89% with either the first or second prediction. The map visualization component helped to reduce the biological and mathematical complexity of the test into an easy to understand format for practicing physicians. The map- based approach allowed a fuzzy prediction that complements a class-based prediction and provides substantial additional information on the relationship between an unknown specimen and other related specimens of known provenance. Conclusion: CUP is a formidable clinical problem; correctly identifying the primary site and rendering specific treatment translates into improved patient outcomes. The use of an SOM to depict the genomic profile of the tumor specimen makes it easier for the clinician or pathologist to understand what tumor type the CUP most closely resembles and facilitates further diagnostic or therapeutic decisions.

No significant financial relationships to disclose.

Molecular identification of carcinoma of unknown primary (CUP) with gene expression profiling

21024

Background: We previously reported a method for determining the site of tumor origin for CUP by comparing a 92- gene expression profile to that in a database created from 600 primary and metastatic tumor bank specimens of known origin. K-nearest neighbor analysis was used to determine the likelihood of an unknown patient specimen originating from a particular site with the likelihood assigned as a confidence level and reported as high, medium, low, or unclassified. Herein, we report the analysis of the gene expression profiling results from our initial series of clinical CUP specimens. Methods: We reviewed the results of 76 consecutive de-identified patient samples submitted to our laboratory for routine CUP testing. RNA was extracted from the formalin-fixed, paraffin-embedded (FFPE) tissue blocks and cDNA products used in a semi-quantitative real-time PCR to detect 87 tumor-associated genes and 5 reference genes. Gene expression data were then compared with our database and k-nearest neighbor analysis used to identify the 5 closest neighbors. If all 5 or 4/5 were the same, the result was classified as “high likelihood”, 3/5 = “moderate likelihood”, 2/5 = “low likelihood” and none matching was “unclassifiable”. Results: For the 76 clinical CUP samples tested, gene profiling analysis yielded high-likelihood predictions for 34 (45%), moderate for 12 (16%), low for 12 (16%), and unclassified for 14 (18%); amplification was inadequate for 4 (5%) samples. Overall, gene profiling analysis yielded classifiable predictions in 58 (76%) of clinical CUP samples. An occult carcinoid, metastatic melanoma and adenocarcinoma of the endocervix were identified and then found clinically using this assay. Conclusions: Our previous findings indicate that gene expression profiling can correctly identify the site of tumor origin in a high percentage of tumor bank samples. Data from the present study suggests that this approach can identify a primary site of tumor origin in 76% of actual clinical specimens from pathologist-submitted CUP cases.

No significant financial relationships to disclose.

A multiplex assay for detection of common pediatric sarcoma tumor markers

10041

Background: Molecular assays for tumor markers have become an important component in diagnosing pediatric sarcomas and small round cell tumors. We developed a multiplex assay to detect 7 common translocations associated with synovial sarcoma (SYT/SSX1, SYT/SSX2), Ewing's sarcoma (EWS/FLI1, EWS/ERG), rhabdomyosarcoma (PAX3/FKHR, PAX7/FKHR), and small round cell desmoplastic tumors (SRCDT) (EWS/WT1). Methods: 27 samples were analyzed with the multiplex assay: 13 formalin-fixed paraffin-embedded tumor samples, 5 fresh frozen tumor samples, 2 commercial RNA samples (SYT/SSX1, SYT/SSX2), 3 cell line samples (EWS/FLI, EWS/ERG, PAX3/FKHR), 1 synthetic control (PAX7/FKHR), and 3 negative controls. After RNA extraction, RT-PCR was performed using the SuperScript III One-Step RT-PCR System with Platinum Taq DNA Polymerase (Invitrogen, Carlsbad, CA). 12 primers were added to a single master mix to amplify all 7 translocations and an internal control; 1 primer from each pair was fluorescently labeled. After RT-PCR, the PCR products were separated on a genetic analyzer and the translocations identified based on the size of the PCR products and their signal intensity. Samples were also analyzed by our current assay (real-time RT-PCR or standard RT-PCR/gel electrophoresis). Results: The results of our current and multiplex assays were positive for all synthetic controls, cell lines, and commercial RNA samples and were concordant for 15/18 tumor samples: 2/7 synovial sarcoma samples were positive for SYT/SSX1 and 3/7 for SYT/SSX2; 2/6 Ewing's sarcoma samples were EWS/FLI1-positive; 1/1 SRCDT sample was EWS/WT1-positive; and 4/4 rhabdomyosarcoma samples were negative. The 3 discordant samples tested negative with our current assay; the new multiplex assay detected EWS/FLI1 in 1 of these and SYT/SSX2 in 2, in agreement with the histological classification. Conclusions: This multiplex assay can detect 7 translocations commonly found in pediatric soft tissue tumors in a single-tube reaction, with increased clinical sensitivity relative to our current methods.

No significant financial relationships to disclose.

Real-time reverse transcription-polymerase chain reaction for detection of SYT-SSX translocation in synovial sarcoma

9553

Background: Synovial sarcoma is the most common non-rhabdomyosarcomatous soft tissue sarcoma in children and adolescents. A specific translocation, t(X;18), induces fusion of the SYT gene on chromosome 18 to an SSX gene on chromosome X. The resulting fusion gene consists of at least 2 subtypes with different breakpoints: SYT-SSX1(X;18)(p11.23;q11.2) and SYT-SSX2 (X;18)(p11.21;q11.2). Because t(X;18) transcripts occur in >90% of synovial sarcoma subtypes, this marker may be useful for diagnosis. We evaluated the accuracy of a multiplex real-time reverse transcription-polymerase chain reaction (RT-PCR) assay for detection of the primary SYT-SSX fusion transcript types in formalin-fixed, paraffin-embedded (FFPE) tissues and frozen tissues. Methods: 17 tumors (7 synovial sarcomas, 4 Ewing’s sarcomas, 5 rhabdomyosarcomas, 1 small round blue-cell tumor), 4 normal tissues, and 4 control samples were tested for SYT-SSX translocations using real-time RT-PCR. Results were compared to those obtained with gel electrophoresis detection of amplified transcripts; discrepant results were confirmed by sequencing. Results: Concordance between real time RT-PCR and gel electrophoresis was 100% (25/25) for internal control genes and SYT-SSX1, and 92% (23/25) for SYT-SSX2. Of the 2 samples with discordant SYT-SSX2 results, 1 was positive by real-time RT-PCR but not gel electrophoresis and 1 was positive by electrophoresis but not real-time RT-PCR; in both cases, DNA sequencing confirmed the real-time RT-PCR results. The minimum percentage of tumor to normal cells required for detection of SYT-SSX fusion transcripts by real-time RT-PCR was 6.25%. Conclusions: This real-time RT-PCR assay appears to provide greater accuracy than gel electrophoresis for identification of SYT-SSX translocation and fusion types.

No significant financial relationships to disclose.

Distribution of UGT1A1 (TA) polymorphisms in Caucasian and Asian subjects

2063

Background: The hepatic isoform 1A1 of uridine diphosphate glucuronosyltransferase (UGT) is responsible for glucuronidation and detoxification of SN-38, the active metabolite of irinotecan. The presence of an additional TA repeat in the TATA sequence of the UGT1A1 gene is a common polymorphism, leading to a significant decrease in SN-38 glucuronidation. Patients with the UGT1A1 (TA)7 allele (either [TA]6/7 or [TA]7/7 ) are more likely to experience severe neutropenia and diarrhea following irinotecan chemotherapy. We assessed the distribution of the UGT1A1 (TA) polymorphism in Caucasian and Asian subjects. Methods: We used a fluorescent PCR-based assay to detect UGT1A1 (TA) polymorphisms in 129 healthy subjects (52 Caucasian, 34 Chinese, 36 Filipino, and 7 Japanese). The chi-square test was used to assess between-group differences in the distribution of UGT1A1 (TA) genotypes. Results: UGT1A1 (TA) genotype distribution differed significantly between Caucasian and Asian subjects (P = 0.003). The UGT1A1 (TA)6/7 and (TA)7/7 genotypes were more common in Caucasians than Asians. Genotype distributions did not differ significantly between men and women in either group ( Table ). Conclusions: The frequency of the deleterious UGT1A1 (TA)7 polymorphism was greater in Caucasians than in Asians; genotype frequencies were consistent with previous reports. In both groups, UGT1A1 (TA) genotype distributions were similar in men and women.

[Table: see text]

No significant financial relationships to disclose.

Detection of seven polymorphisms associated with colorectal cancer therapeutic response and toxicity

13160

Background: First-line therapy for metastatic colorectal cancer (CRC) is 5-fluorouracil/leucovorin in combination with oxaliplatin (ie, FOLFOX™) or irinotecan (ie, FOLFIRI). Optimizing this therapy for an individual patient, however, is complicated due to wide variability in drug response and potential for toxicity. Such variability may be due to functional genomic polymorphisms in the drug target gene or in the metabolizing or DNA repair enzyme genes. We report, herein, development and validation of 2 new assays that, together, detect 7 polymorphisms associated with CRC drug response and toxicity. Methods: The first assay (SNaPshot) simultaneously detects 4 polymorphisms by using primers targeting the ERCC1, XPD, GST-P1, and XRCC-1 genes, single nucleotide primer extension of PCR products, electrophoresis and fluorescent detection on an ABI PRISM® 3100 Genetic Analyzer, and data analysis using GeneMapper® software (Applied Biosystems, Inc.). The second assay (F-PCR) simultaneously detects 3 polymorphisms using paired primers targeting the TS and UGT1A1 genes. One primer per pair is labeled with a fluorescent tag, and electrophoresis, detection, and data analysis are performed as described for the SNaPshot assay. Results: Based on fragment size and color, the intra- and interassay precision for SnaPshot ranged from 0.04%-0.51% and 0.14%-0.59%, respectively, and for F-PCR from 0.02%-0.16% and 0.09%-0.29%, respectively. There was 100% concordance in the genotypes determined in 3 separate SNaPshot (n=44 samples) and F-PCR (n=32 samples) assays. Furthermore, there was 100% agreement between genotypes determined by the SNaPshot method and those determined by RFLP (n=10) and between genotypes determined by the F-PCR method and those determined by pyrosequencing (n=17). Conclusions: Our multiplex SNaPshot and F-PCR methods can accurately detect 7 polymorphisms associated with CRC drug response and toxicity. These multiplex PCRs should lead to improved precision and ease of interpretation relative to that of single PCR methods. These methods may help the clinician optimize CRC therapy for individual patients.

No significant financial relationships to disclose.

Hippocampal corticotropin releasing hormone: pre- and postsynaptic location and release by stress

Neuropeptides modulate neuronal function in hippocampus, but the organization of hippocampal sites of peptide release and actions is not fully understood. The stress-associated neuropeptide corticotropin releasing hormone (CRH) is expressed in inhibitory interneurons of rodent hippocampus, yet physiological and pharmacological data indicate that it excites pyramidal cells. Here we aimed to delineate the structural elements underlying the actions of CRH, and determine whether stress influenced hippocampal principal cells also via actions of this endogenous peptide. In hippocampal pyramidal cell layers, CRH was located exclusively in a subset of GABAergic somata, axons and boutons, whereas the principal receptor mediating the peptide's actions, CRH receptor 1 (CRF1), resided mainly on dendritic spines of pyramidal cells. Acute 'psychological' stress led to activation of principal neurons that expressed CRH receptors, as measured by rapid phosphorylation of the transcription factor cyclic AMP responsive element binding protein. This neuronal activation was abolished by selectively blocking the CRF1 receptor, suggesting that stress-evoked endogenous CRH release was involved in the activation of hippocampal principal cells.

Roles of glutamate synthase, gltBD, and gltF in nitrogen metabolism of Escherichia coli and Klebsiella aerogenes

Mutants of Escherichia coli and Klebsiella aerogenes that are deficient in glutamate synthase (glutamate-oxoglutarate amidotransferase [GOGAT]) activity have difficulty growing with nitrogen sources other than ammonia. Two models have been proposed to account for this inability to grow. One model postulated an imbalance between glutamine synthesis and glutamine degradation that led to a repression of the Ntr system and the subsequent failure to activate transcription of genes required for the use of alternative nitrogen sources. The other model postulated that mutations in gltB or gltD (which encode the subunits of GOGAT) were polar on a downstream gene, gltF, which is necessary for proper activation of gene expression by the Ntr system. The data reported here show that the gltF model is incorrect for three reasons: first, a nonpolar gltB and a polar gltD mutation of K. aerogenes both show the same phenotype; second, K. aerogenes and several other enteric bacteria lack a gene homologous to gltF; and third, mutants of E. coli whose gltF gene has been deleted show no defect in nitrogen metabolism. The argument that accumulated glutamine represses the Ntr system in gltB or gltD mutants is also incorrect, because these mutants can derepress the Ntr system normally so long as sufficient glutamate is supplied. Thus, we conclude that gltB or gltD mutants grow slowly on many poor nitrogen sources because they are starved for glutamate. Much of the glutamate formed by catabolism of alternative nitrogen sources is converted to glutamine, which cannot be efficiently converted to glutamate in the absence of GOGAT activity. Finally, GOGAT-deficient E. coli cells growing with glutamine as the sole nitrogen source increase their synthesis of the other glutamate-forming enzyme, glutamate dehydrogenase, severalfold, but this is still insufficient to allow rapid growth under these conditions.

Novel and transient populations of corticotropin-releasing hormone-expressing neurons in developing hippocampus suggest unique functional roles: a quantitative spatiotemporal analysis

Robust physiological actions of the neuropeptide corticotropin-releasing hormone (CRH) on hippocampal pyramidal neurons have been demonstrated, which may contribute to synaptic efficacy and to learning and memory processes. These excitatory actions of the peptide, as well as the expression of the CRH receptor type that mediates them, are particularly prominent during early postnatal life, suggesting that endogenous CRH may contribute to processes involved in maturation of hippocampal circuitry. To further elucidate the function(s) of endogenous CRH in developing hippocampus, we used neurochemical and quantitative stereological methods to characterize in detail CRH-expressing neuronal populations during postnatal hippocampal differentiation. These experiments revealed progressively increasing numbers of CRH-expressing neurons in developing hippocampus that peaked on postnatal day 11-18 and then declined drastically to adult levels. These cells belonged to several discrete populations, distinguished by GAD67 mRNA expression, morphology, and distinct spatiotemporal distribution profiles. Importantly, a novel population of Cajal-Retzius-like CRH-expressing neurons was characterized that exists only transiently in early postnatal hippocampus and is positioned to contribute to the establishment of hippocampal connectivity. These findings suggest novel, age-specific roles for CRH in regulating early developmental events in the hippocampal formation.

Growth inhibition caused by overexpression of the structural gene for glutamate dehydrogenase (gdhA) from Klebsiella aerogenes

Two linked mutations affecting glutamate dehydrogenase (GDH) formation (gdh-1 and rev-2) had been isolated at a locus near the trp cluster in Klebsiella aerogenes. The properties of these two mutations were consistent with those of a locus containing either a regulatory gene or a structural gene. The gdhA gene from K. aerogenes was cloned and sequenced, and an insertion mutation was generated and shown to be linked to trp. A region of gdhA from a strain bearing gdh-1 was sequenced and shown to have a single-base-pair change, confirming that the locus defined by gdh-1 is the structural gene for GDH. Mutants with the same phenotype as rev-2 were isolated, and their sequences showed that the mutations were located in the promoter region of the gdhA gene. The linkage of gdhA to trp in K. aerogenes was explained by postulating an inversion of the genetic map relative to other enteric bacteria. Strains that bore high-copy-number clones of gdhA displayed an auxotrophy that was interpreted as a limitation for alpha-ketoglutarate and consequently for succinyl-coenzyme A (CoA). Three lines of evidence supported this interpretation: high-copy-number clones of the enzymatically inactive gdhA1 allele showed no auxotrophy, repression of GDH expression by the nitrogen assimilation control protein (NAC) relieved the auxotrophy, and addition of compounds that could increase the alpha-ketoglutarate supply or reduce the succinyl-CoA requirement relieved the auxotrophy.

Enhanced CREB phosphorylation in immature dentate gyrus granule cells precedes neurotrophin expression and indicates a specific role of CREB in granule cell differentiation

Differentiation and maturation of dentate gyrus granule cells requires coordinated interactions of numerous processes. These must be regulated by protein factors capable of integrating signals mediated through diverse signalling pathways. Such integrators of inter and intracellular physiological stimuli include the cAMP-response element binding protein (CREB), a leucine-zipper class transcription factor that is activated through phosphorylation. Neuronal activity and neurotrophic factors, known to be involved in granule cell differentiation, are major physiologic regulators of CREB function. To examine whether CREB may play a role in governing coordinated gene transcription during granule cell differentiation, we determined the spatial and temporal profiles of phosphorylated (activated) CREB throughout postnatal development in immature rat hippocampus. We demonstrate that CREB activation is confined to discrete, early stages of granule cell differentiation. In addition, CREB phosphorylation occurs prior to expression of the neurotrophins BDNF and NT-3. These data indicate that in a signal transduction cascade connecting CREB and neurotrophins in the process of granule cell maturation, CREB is located upstream of neurotrophins. Importantly, CREB may be a critical component of the machinery regulating the coordinated transcription of genes contributing to the differentiation of granule cells and their integration into the dentate gyrus network.

Nitrogen regulatory protein C-controlled genes of Escherichia coli: scavenging as a defense against nitrogen limitation

Nitrogen regulatory protein C (NtrC) of enteric bacteria activates transcription of genes/operons whose products minimize the slowing of growth under nitrogen-limiting conditions. To reveal the NtrC regulon of Escherichia coli we compared mRNA levels in a mutant strain that overexpresses NtrC-activated genes [glnL(Up)] to those in a strain with an ntrC (glnG) null allele by using DNA microarrays. Both strains could be grown under conditions of nitrogen excess. Thus, we could avoid differences in gene expression caused by slow growth or nitrogen limitation per se. Rearranging the spot images from microarrays in genome order allowed us to detect all of the operons known to be under NtrC control and facilitated detection of a number of new ones. Many of these operons encode transport systems for nitrogen-containing compounds, including compounds recycled during cell-wall synthesis, and hence scavenging appears to be a primary response to nitrogen limitation. In all, approximately 2% of the E. coli genome appears to be under NtrC control, although transcription of some operons depends on the nitrogen assimilation control protein, which serves as an adapter between NtrC and final sigma(70)-dependent promoters.

The amino-terminal 100 residues of the nitrogen assimilation control protein (NAC) encode all known properties of NAC from Klebsiella aerogenes and Escherichia coli

The nitrogen assimilation control protein (NAC) from Klebsiella aerogenes or Escherichia coli (NACK or NACE, respectively) is a transcriptional regulator that is both necessary and sufficient to activate transcription of the histidine utilization (hut) operon and to repress transcription of the glutamate dehydrogenase (gdh) operon in K. aerogenes. Truncated NAC polypeptides, generated by the introduction of stop codons within the nac open reading frame, were tested for the ability to activate hut and repress gdh in vivo. Most of the NACK and NACE fragments with 100 or more amino acids (wild-type NACK and NACE both have 305 amino acids) were functional in activating hut and repressing gdh expression in vivo. Full-length NACK and NACE were isolated as chimeric proteins with the maltose-binding protein (MBP). NACK and NACE released from such chimeras were able to activate hut transcription in a purified system in vitro, as were NACK129 and NACE100 (a NACK fragment of 129 amino acids and a NACE fragment of 100 amino acids) released from comparable chimeras. A set of NACE and NACK fragments carrying nickel-binding histidine tags (his6) at their C termini were also generated. All such constructs derived from NACE were insoluble, as was NACE itself. Of the his6-tagged constructs derived from NACK, NACK100 was inactive, but NACK120 was active. Several NAC fragments were tested for dimerization. NACK120-his6 and NACK100-his6 were dimers in solution. MBP-NACK and MBP-NACK129 were monomers in solution but dimerized when the MBP was released by cleavage with factor Xa. MBP-NACE was readily cleaved by factor Xa, but the resulting NACE was also degraded by the protease. However, MBP-NACE-his6 was completely resistant to cleavage by factor Xa, suggesting an interaction between the C and N termini of this protein.

Two roles for the leucine-responsive regulatory protein in expression of the alanine catabolic operon (dadAB) in Klebsiella aerogenes

The lrp gene, which codes for the leucine-responsive regulatory protein (Lrp), was cloned from Klebsiella aerogenes W70. The DNA sequence was determined, and the clone was used to create a disruption of the lrp gene. The lack of functional Lrp led to an increased expression of the alanine catabolic operon (dad) in the absence of the inducer L-alanine but also to a decreased expression of the operon in the presence of L-alanine. Thus, Lrp is both a repressor and activator of dad expression. Lrp is also necessary for glutamate synthase formation but not for the formation of two other enzymes controlled by the nitrogen regulatory (Ntr) system, glutamate dehydrogenase and histidase.

The nac (nitrogen assimilation control) gene from Escherichia coli

The nitrogen assimilation control gene, nac, was detected in Escherichia coli but not in Salmonella typhimurium by Southern blotting, using a probe from the Klebsiella aerogenes nac (nacK) gene. The E. coli nac gene (nacE) was isolated from a cosmid clone by complementation of a nac mutation in K. aerogenes. nacE was fully functional in this complementation assay. DNA sequence analysis showed considerable divergence between nacE and nacK, with a predicted amino acid sequence identity of only 79% and most of the divergence in the C-terminal half of the protein sequence. The total predicted size of NAC(E) is 305 amino acids, the same as for NAC(K). A null mutation, nac-28, was generated by reverse genetics. Mutants bearing nac-28 have a variety of phenotypes related to nitrogen metabolism, including slower growth on cytosine, faster growth on arginine, and suppression of the failure of an Ntr-constitutive mutant to grow with serine as sole nitrogen source. In addition to a loss of nitrogen regulation of histidase formation, nac-28 mutants also showed a loss of a weak repression of glutamate dehydrogenase formation. This repression was unexpected because it is balanced by a NAC-independent activation of glutamate dehydrogenase formation during nitrogen-limited growth. Attempts to purify NAC(E) by using methods established for NAC(K) failed, and NAC(E) appears to be degraded with a half-life at 30 degrees C as short as 15 min during inhibition of protein synthesis.

Genetic analysis, using P22 challenge phage, of the nitrogen activator protein DNA-binding site in the Klebsiella aerogenes put operon

The nac gene product is a LysR regulatory protein required for nitrogen regulation of several operons from Klebsiella aerogenes and Escherichia coli. We used P22 challenge phage carrying the put control region from K. aerogenes to identify the nucleotide residues important for nitrogen assimilation control protein (NAC) binding in vivo. Mutations in an asymmetric 30-bp region prevented DNA binding by NAC. Gel retardation experiments confirmed that NAC specifically binds to this sequence in vitro, but NAC does not bind to the corresponding region from the put operon of Salmonella typhimurium, which is not regulated by NAC.

Two roles for the DNA recognition site of the Klebsiella aerogenes nitrogen assimilation control protein

The nitrogen assimilation control protein (NAC) binds to a site within the promoter region of the histidine utilization operon (hutUH) of Klebsiella aerogenes, and NAC bound at this site activates transcription of hutUH. This NAC-binding site was characterized by a combination of random and directed DNA mutagenesis. Mutations that abolished or diminished in vivo transcriptional activation by NAC were found to lie within a 15-bp region contained within the 26-bp region protected by NAC from DNase I digestion. This 15-bp core has the palindromic ends ATA and TAT, and it matches the consensus for LysR family transcriptional regulators. Protein-binding experiments showed that transcriptional activation in vivo decreased with decreasing binding in vitro. In contrast to the NAC-binding site from hutUH, the NAC-binding site from the gdhA promoter failed to activate transcription from a semisynthetic promoter, and this failure was not due to weak binding or greatly distorted protein-DNA structure. Mutations in the promoter-proximal half-site of the NAC-binding site from gdhA allowed this site to activate transcription. Similar studies using the NAC-binding site from hut showed that two mutations in the promoter proximal half-site increased binding but abolished transcriptional activation. Interestingly, for symmetric mutations in the promoter-distal half-site, loss of transcriptional activation was always correlated with a decrease in binding. We conclude from these observations that if the binding in vitro reflects the binding in vivo, then binding of NAC to DNA is not sufficient for transcriptional activation and that the NAC-binding site can be functionally divided in two half-sites, with related but different functions.

Alanine catabolism in Klebsiella aerogenes: molecular characterization of the dadAB operon and its regulation by the nitrogen assimilation control protein

Klebsiella aerogenes strains with reduced levels of D-amino acid dehydrogenase not only fail to use alanine as a growth substrate but also become sensitive to alanine in minimal media supplemented with glucose and ammonium. The inability of these mutant strains to catabolize the alanine provided in the medium interferes with both pathways of glutamate production. Alanine derepresses the nitrogen regulatory system (Ntr), which in turn represses glutamate dehydrogenase, one pathway of glutamate production. Alanine also inhibits the enzyme glutamine synthetase, the first enzyme in the other pathway of glutamate production. Therefore, in the presence of alanine, strains with mutations in dadA (the gene that codes for a subunit of the dehydrogenase) exhibit a glutamate auxotrophy when ammonium is the sole source of nitrogen. The alanine catabolic operon of Klebsiella aerogenes, dadAB, was cloned, and its DNA sequence was determined. The clone complemented the alanine defects of dadA strains. The operon has a high similarity to the dadAB operon of Salmonella typhimurium and the dadAX operon of Escherichia coli, each of which codes for the smaller subunit of D-amino acid dehydrogenase and the catabolic alanine racemase. Unlike the cases for E. coli and S. typhimurium, the dad operon of K. aerogenes is activated by the Ntr system, mediated in this case by the nitrogen assimilation control protein (NAC). A sequence matching the DNA consensus for NAC-binding sites is located centered at position -44 with respect to the start of transcription. The promoter of this operon also contains consensus binding sites for the catabolite activator protein and the leucine-responsive regulatory protein.

Repression of the Klebsiella aerogenes nac promoter

Transcription of the nitrogen-regulated nac promoter of Klebsiella aerogenes requires sigma54 RNA polymerase, is activated by the phosphorylated form of the transcription factor nitrogen regulator I (NRI) (NtrC), and is repressed by the product of the nac gene, Nac. Nac protects a large portion of the nac control region, extending from positions -130 to -70, from digestion by DNase I. This site(s) lies immediately upstream from the site at which sigma 54 RNA polymerase binds, is downstream of a high-affinity binding site for the transcriptional activator NRI approximately P, and partially overlaps a low-affinity NRI approximately P-binding site. Binding of Nac to the DNA resulted in bending of the DNA but did not interfere with the binding of sigma 54 RNA polymerase to the promoter or with the binding of NRI approximately P to either the high-affinity site or low-affinity site. Furthermore, transcription assays with various wild-type and mutant templates suggested that Nac did not exclude NRI approximately P from either the low- or high-affinity sites, nor did Nac interfere with the ability of the polymerase to form the open complex when the binding sites for NRI approximately P were moved to different locations upstream from the promoter. Rather, Nac seemed to repress by an antiactivation mechanism in which the interaction of the NRI approximately P, bound at its normal sites, with sigma 54 RNA polymerase, bound to the promoter, was prevented.

Activation of transcription initiation from the nac promoter of Klebsiella aerogenes

The nac gene of Klebsiella aerogenes encodes a bifunctional transcription factor that activates or represses the expression of several operons under conditions of nitrogen limitation. In experiments with purified components, transcription from the nac promoter was initiated by sigma 54 RNA polymerase and was activated by the phosphorylated form of nitrogen regulator I (NRI) (NtrC). The activation of the nac promoter required a higher concentration of NRI approximately P than did the activation of the Escherichia coli glnAp2 promoter, and both the promoter and upstream enhancer element contributed to this difference. The nac promoter had a lower affinity for sigma 54 RNA polymerase than did glnAp2, and uninitiated competitor-resistant transcription complexes formed at the nac promoter decayed to competitor-sensitive complexes at a greater rate than did similar complexes formed at the glnAp2 promoter. The nac enhancer, consisting of a single high-affinity NRI-binding site and an adjacent site with low affinity for NRI, was less efficient in stimulating transcription than was the glnA enhancer, which consists of two adjacent high-affinity NRI-binding sites. When these binding sites were exchanged, transcription from the nac promoter was increased and transcription from the glnAp2 promoter was decreased at low concentrations of NRI approximately P. Another indication of the difference in the efficiency of these enhancers is that although activation of a nac promoter construct containing the glnA enhancer was relatively insensitive to subtle alterations in the position of these sites relative to the position of the promoter, activation of the natural nac promoter or a nac promoter construct containing only a single high-affinity NRI approximately P binding site was strongly affected by subtle alterations in the position of the NRI approximately P binding site(s), indicating a face-of-the-helix dependency for activation.

Activation of the Escherichia coli lacZ promoter by the Klebsiella aerogenes nitrogen assimilation control protein (NAC), a LysR family transcription factor

A chimeric promoter with the nitrogen assimilation control protein binding site from hutUp of Klebsiella aerogenes fused to the lacZ core promoter from Escherichia coli was built and cloned in a lacZ reporter plasmid. This construct showed a 14-fold increase of beta-galactosidase activity upon nitrogen limitation. Primer extension experiments showed that the nitrogen assimilation control protein activates lacZp1 in a position-dependent manner.

The nitrogen assimilation control protein, NAC, is a DNA binding transcription activator in Klebsiella aerogenes

A 32-kDa polypeptide corresponding to NAC, the product of the Klebsiella aerogenes nac gene, was overexpressed from a plasmid carrying a tac'-'nac operon fusion and purified to near homogeneity by taking advantage of its unusual solubility properties. NAC was able to shift the electrophoretic migration of DNA fragments carrying the NAC-sensitive promoters hutUp, putPp1, and ureDp. The interaction between NAC and hutUp was localized to a 26-bp region centered approximately 64 bp upstream of the hutUp transcription initiation site. Moreover, NAC protected this region from DNase I digestion. Mobility shift and DNase I protection studies utilizing the putP and ureD promoter regions identified NAC-binding regions of sizes and locations similar to those found in hutUp. Comparison of the DNA sequences which were protected from DNase I digestion by NAC suggests a minimal NAC-binding consensus sequence: 5'-ATA-N9-TAT-3'. In vitro transcription assays demonstrated that NAC was capable of activating the transcription of hutUp by sigma 70-RNA polymerase holoenzyme when this promoter was presented as either a linear or supercoiled DNA molecule. Thus, NAC displays the in vitro DNA-binding and transcription activation properties which have been predicted for the product of the nac gene.

Roles of catabolite activator protein sites centered at -81.5 and -41.5 in the activation of the Klebsiella aerogenes histidine utilization operon hutUH

The Klebsiella aerogenes hutUH operon is preceded by a promoter region, hut(P), that contains two divergent promoters (hutUp and Pc) which overlap and are alternately expressed. In the absence of the catabolite gene activator protein-cyclic AMP (CAP-cAMP) complex, Pc is predominantly expressed while hutUp is largely repressed. CAP-cAMP has the dual effect of repressing transcription from Pc while simultaneously activating transcription from hutUp. DNA deletion mutations in this region were used to identify DNA sequences required for transcription of these two promoters. We showed that inactivation of Pc by DNA deletion did not result in activation of hutUp in vitro or in vivo. In addition, Escherichia coli CAP mutants that are known to bind and bend DNA normally but are unable to activate various CAP-dependent promoters were also unable to activate hutUp in vivo. These results invalidate an indirect activation model by which CAP-mediated repression of Pc in itself would led to activation of hutUp. Gel retardation asays with various deletion mutations of hut(P) and DNase I protection analyses revealed a high-affinity CAP binding site (CAP site 1) centered at -81.5 relative to the hutUp start of transcription and a second low-affinity CAP site (CAP site 2) centered at about -41.5. CAP site 1 is essential for activation of hutUp. Although CAP site 2 by itself is unable to activate hutUp in vivo under catabolite-activating conditions, it appears to be required for maximal transcription from a site centered at -41.5, does not activate hutUp suggests that the role of CAP-cAMP at the weaker CAP site may be different from that of other promoters containing a similarly positioned site. We propose that CAP directly stimulates the activity of RNA polymerase at hutUp and that this reaction is completely dependent on a naturally occurring CAP site centered at -81.5 and also involves a second CAP site centered at about -41.5 for maximal activation.

Identification of the hutUH operator (hutUo) from Klebsiella aerogenes by DNA deletion analysis

Expression of Klebsiella aerogenes histidine utilization operons hutUH and hutIG is negatively regulated by the product of hutC. Multiple copies of the hutUH promoter region [hut(P)] present in trans were able to titrate the limited amount of host-encoded hut repressor (HutC). Thus, the hut(P) region contains a specific binding site for HutC. To identify DNA sequences required for HutC titration, we constructed and characterized a set of 40 left-entering and 28 right-entering deletions within a 250-bp DNA sequence containing the hut(P) region. Mutants carrying deletions that altered a unique dyad symmetric sequence, ATGCTTGTATAGACAAGTAT, from -11 to -30 relative to the hutUH promoter (hutUp) were unable to titrate hut repressor; mutants carrying deletions that left this sequence intact retained their ability to titrate hut repressor. Thus, we identify ATGCTTGT ACAAGTAT as the hutUH operator.

The product of the Klebsiella aerogenes nac (nitrogen assimilation control) gene is sufficient for activation of the hut operons and repression of the gdh operon

In Klebsiella aerogenes, the formation of a large number of enzymes responds to the quality and quantity of the nitrogen source provided in the growth medium, and this regulation requires the action of the nitrogen regulatory (NTR) system in every case known. Nitrogen regulation of several operons requires not only the NTR system, but also NAC, the product of the nac gene, raising the question of whether the role of NAC is to activate operons directly or by modifying the specificity of the NTR system. We isolated an insertion of the transposon Tn5tac1 which puts nac gene expression under the control of the IPTG-inducible tac promoter rather than the nitrogen-responsive nac promoter. When IPTG was present, cells carrying the tac-nac fusion activated NAC-dependent operons and repressed NAC-repressible operons independent of the nitrogen supply and even in the absence of an active NTR system. Thus, NAC is sufficient to regulate operons like hut (encoding histidase) and gdh (encoding glutamate dehydrogenase), confirming the model that the NTR system activates nac expression and NAC activates hut and represses gdh. Activation of urease formation occurred at a lower level of NAC than that required for glutamate dehydrogenase repression, and activation of histidase formation required still more NAC.

The nac (nitrogen assimilation control) gene from Klebsiella aerogenes

The Klebsiella aerogenes nac gene, whose product is necessary for nitrogen regulation of a number of operons, was identified and its DNA sequence determined. The nac sequence predicted a protein a 305 amino acids with a strong similarity to members of the LysR family of regulatory proteins, especially OxyR from Escherichia coli. Analysis of proteins expressed in minicells showed that nac is a single-gene operon whose product has an apparent molecular weight of about 32 kDa as measured in sodium dodecyl sulfate-polyacrylamide gel electrophoresis. Immediately downstream from nac is a two-gene operon, the first gene of which encodes another member of the LysR family. Upstream from nac is a tRNAAsn gene transcribed divergently from nac. About 60 bp upstream from the nac open reading frame lies a sequence nearly identical to the consensus for sigma 54-dependent promoters, with the conserved GG and GC nucleotides at -26 and -14 relative to the start of transcription. About 130 bp farther upstream (at -153 relative to the start of transcription) is a sequence nearly identical to the transcriptional activator NTRC-responsive enhancer consensus. Another weaker NTRC-binding site is located adjacent to this site (at -133 relative to the start of transcription). Thus, we propose that nac is transcribed by RNA polymerase carrying sigma 54 in response to the nitrogen regulatory (NTR) system. A transposon located between the promoter and the nac ORF prevented NTR-mediated expression of nac, supporting this identification of the promoter sequence. The insertion of over 5 kb of transposon DNA between the enhancer and its target promoter had only a weak effect on enhancer-mediated regulation, suggesting that enhancers may be able to act at a considerable distance on the bacterial chromosome.