Effect of empagliflozin on cardiac remodelling in South Asian and non-South Asian individuals: insights from the EMPA-HEART CardioLink-6 randomised clinical trial

BACKGROUND

This exploratory sub-analysis of the EMPA-HEART CardioLink-6 trial examined whether the previously reported benefit of the sodium-glucose cotransporter 2 (SGLT2) inhibitor empagliflozin on left ventricular (LV) mass (LVM) regression differs between individuals of South Asian and non-South Asian ethnicity.

METHODS

EMPA-HEART CardioLink-6 was a double-blind, placebo-controlled clinical trial that randomised 97 individuals with type 2 diabetes mellitus (T2DM) and coronary artery disease (CAD) to either empagliflozin 10 mg daily or placebo for 6 months. LV parameters and function were assessed using cardiac magnetic resonance imaging. The 6-month changes in LVM and LV volumes, all indexed to baseline body surface area, for South Asian participants were compared to those for non-South Asian individuals.

RESULTS

Compared to the non-South Asian group, the South Asian sub-cohort comprised more males, was younger and had a lower median body mass index. The adjusted difference for LVMi change over 6 months was -4.3 g/m2 (95% confidence interval [CI], -7.5, -1.0; P = 0.042) for the South Asian group and -2.3 g/m2 (95% CI, -6.4, 1.9; P = 0.28) for the non-South Asian group (Pinteraction = 0.45). There was no between-group difference for the adjusted differences in baseline body surface area-indexed LV volumes and LV ejection fraction.

CONCLUSIONS

There was no meaningful difference in empagliflozin-associated LVM regression between South Asian and non-South Asian individuals living with T2DM and CAD in the EMPA-HEART CardioLink-6 trial.

TRIAL REGISTRATION

ClinicalTrials.gov Identifier: NCT02998970 (First posted on 21/12/ 2016).

Attitudes Among Society of Women in Urology Members Toward Dobbs v. Jackson Women's Health Organization

OBJECTIVE

To evaluate attitudes of women in urology regarding the Supreme Court ruling Dobbs v. Jackson Women's Health Organization, including impacts on personal/professional decision-making and the urology workforce.

METHODS

An IRB-exempt survey including Likert questions on participant views and free text questions was distributed to 1200 members of the Society of Women in Urology on 9/2/2022. Participants were medical students, urology residents, fellows, and practicing/retired urologists over 18. Responses were anonymous and aggregated. Quantitative responses were characterized with descriptive statistics and free-text responses were analyzed using thematic mapping. To complement this analysis, urologist density was mapped by county using 2021 National Provider Identifier data. State abortion laws were categorized based on Guttmacher Institute data on 10/20/2022. Data were analyzed using logistic regression, Poisson regression, and multiple linear regression.

RESULTS

329 respondents completed the survey. 88% disagree/strongly disagree with the Dobbs ruling. 42% of trainees may have changed their rank list if current abortion laws existed during their match. 60% of respondents said Dobbs will impact where they choose their next job. 61.5% of counties had zero urologists in 2021, 76% of which were in states with restrictive abortion laws. Urologist density was inversely associated with abortion law restrictiveness compared with the most protective counties.

CONCLUSION

The Dobbs ruling will significantly impact the urology workforce. Trainees may change how they rank programs in states with restrictive abortion laws, and urologists may consider abortion laws when choosing jobs. Restrictive states are at higher risk for worsening access to urologic care.

Providers' perspectives on the reproductive decision-making of BRCA-positive women

BACKGROUND

Reproductive decision-making is difficult for BRCA-positive women. Our objective was to assess the complexities of decision-making and identify decisional supports for patients and providers when discussing reproductive options prior to risk-reducing salpingo-oophorectomy (RRSO).

METHODS

This study was of qualitive design, using data collection via semi-structured interviews conducted from November 2018 to October 2020. Individuals were included if they were identified to provide care to BRCA-positive women. In total, 19 providers were approached and 15 consented to participate. Providers were recruited from three clinics in Toronto, Ontario located at academic centers: [1] A familial ovarian cancer clinic, [2] A familial breast cancer clinic and [3] A fertility clinic, all of which treat carriers of the BRCA1/BRCA2 genetic mutation. The interview guide was developed according to the Ottawa Decision Support Framework and included questions regarding reproductive options available to patients, factors that impact the decision-making process and the role of decisional support. Interviews were transcribed and transcripts were analyzed thematically using NVIVO 12.

RESULTS

Providers identified three major decisions that reproductive-aged women face when a BRCA mutation is discovered: [1] "Do I want children?"; [2] "Do I want to take the chance of passing on this the mutation?"; and [3] "Do I want to carry a child?" Inherent decision challenges that are faced by both providers and patients included difficult decision type, competing options, scientifically uncertain outcomes, and challenging decision timing. Modifiable decisional needs included: inadequate knowledge, unrealistic expectations, unclear values and inadequate support or resources. Identified clinical gaps included counselling time constraints, lack of reliable sources of background information for patients or providers and need for time-sensitive, geographically accessible, and centralized care.

CONCLUSION

Our study identified a need for a patient information resource that can be immediately provided to patients who carry a BRCA genetic mutation. Other suggestions for clinical practice include more time during consultation appointments, adequate follow-up, value-centric counseling, access to psychosocial support, and a specialized decisional coach.

Association of Patient Belief About Success of Antibiotics for Appendicitis and Outcomes: A Secondary Analysis of the CODA Randomized Clinical Trial

Importance

A patient's belief in the likely success of a treatment may influence outcomes, but this has been understudied in surgical trials.

Objective

To examine the association between patients' baseline beliefs about the likelihood of treatment success with outcomes of antibiotics for appendicitis in the Comparison of Outcomes of Antibiotic Drugs and Appendectomy (CODA) trial.

Design, Setting, and Participants

This was a secondary analysis of the CODA randomized clinical trial. Participants from 25 US medical centers were enrolled between May 3, 2016, and February 5, 2020. Included in the analysis were participants with appendicitis who were randomly assigned to receive antibiotics in the CODA trial. After informed consent but before randomization, participants who were assigned to receive antibiotics responded to a baseline survey including a question about how successful they believed antibiotics could be in treating their appendicitis.

Interventions

Participants were categorized based on baseline survey responses into 1 of 3 belief groups: unsuccessful/unsure, intermediate, and completely successful.

Main Outcomes and Measures

Three outcomes were assigned at 30 days: (1) appendectomy, (2) high decisional regret or dissatisfaction with treatment, and (3) persistent signs and symptoms (abdominal pain, tenderness, fever, or chills). Outcomes were compared across groups using adjusted risk differences (aRDs), with propensity score adjustment for sociodemographic and clinical factors.

Results

Of the 776 study participants who were assigned antibiotic treatment in CODA, a total of 425 (mean [SD] age, 38.5 [13.6] years; 277 male [65%]) completed the baseline belief survey before knowing their treatment assignment. Baseline beliefs were as follows: 22% of participants (92 of 415) had an unsuccessful/unsure response, 51% (212 of 415) had an intermediate response, and 27% (111 of 415) had a completely successful response. Compared with the unsuccessful/unsure group, those who believed antibiotics could be completely successful had a 13-percentage point lower risk of appendectomy (aRD, -13.49; 95% CI, -24.57 to -2.40). The aRD between those with intermediate vs unsuccessful/unsure beliefs was -5.68 (95% CI, -16.57 to 5.20). Compared with the unsuccessful/unsure group, those with intermediate beliefs had a lower risk of persistent signs and symptoms (aRD, -15.72; 95% CI, -29.71 to -1.72), with directionally similar results for the completely successful group (aRD, -15.14; 95% CI, -30.56 to 0.28).

Conclusions and Relevance

Positive patient beliefs about the likely success of antibiotics for appendicitis were associated with a lower risk of appendectomy and with resolution of signs and symptoms by 30 days. Pathways relating beliefs to outcomes and the potential modifiability of beliefs to improve outcomes merit further investigation.

Trial Registration

ClinicalTrials.gov Identifier: NCT02800785.

Primordial germ cells do not migrate along nerve fibres in marmoset monkey and mouse embryos

Primordial germ cells (PGCs) are the embryonic precursors of spermatozoa and eggs. In mammals, PGCs arise early in embryonic development and migrate from their tissue of specification over a significant distance to reach their destinations, the genital ridges. However, the exact mechanism of translocation is still debated. A study on human embryos demonstrated a very close spatial association between migrating PGCs and developing peripheral nerves. Thus, it was proposed that peripheral nerves act as guiding structures for migrating PGCs. The goal of the present study is to test whether the association between nerves and PGCs may be a human-specific finding or whether this represents a general strategy to guide PGCs in mammals. Therefore, we investigated embryos of different developmental stages from the mouse and a non-human primate, the marmoset monkey (Callithrix jacchus), covering the phase from PGC emergence to their arrival in the gonadal ridge. Embryo sections were immunohistochemically co-stained for tubulin beta-3 chain (TUBB3) to visualise neurons and Octamer-binding protein 4 (OCT4 (POU5F1)) as marker for PGCs. The distance between PGCs and the nearest detectable neuron was measured. We discovered that in all embryos analysed of both species, the majority of PGCs (>94%) was found at a minimum distance of 50 µm to the closest neuron and, more importantly, that the PGCs had reached the gonads before any TUBB3 signal could be detected in the vicinity of the gonads. In conclusion, our data indicate that PGC migration along peripheral nerves is not a general mechanism in mammals.

Organic Compounds in a Sub-Antarctic Ice Core: A Potential Suite of Sea Ice Markers

Investigation of organic compounds in ice cores can potentially unlock a wealth of new information in these climate archives. We present results from the first ever ice core drilled on sub-Antarctic island Bouvet, representing a climatologically important but understudied region. We analyze a suite of novel and more familiar organic compounds in the ice core, alongside commonly measured ions. Methanesulfonic acid shows a significant, positive correlation to winter sea ice concentration, as does a fatty acid compound, oleic acid. Both may be sourced from spring phytoplankton blooms, which are larger following greater sea ice extent in the preceding winter. Oxalate, formate, and acetate are positively correlated to sea ice concentration in summer, but sources of these require further investigation. This study demonstrates the potential application of organic compounds from the marine biosphere in generating multiproxy sea ice records, which is critical in improving our understanding of past sea ice changes.

YIA19-001: Mechanisms of Diagnostic Delay Among Black women With Endometrial Cancer (EC): Results from Qualitative Interviews and a National Analysis of Healthcare Data

Background: A major contributor to the black-white mortality gap in endometrial cancer (EC) is late stage at diagnosis for black women, which may be driven by delays in diagnosis both prior to and after symptom disclosure. Methods: For phase 1, black women with EC were recruited through oncology clinics and a local cancer support group. In-depth interviews were conducted focused on experiences of menopause, postmenopausal bleeding (PMB), and symptom disclosure, and transcripts coded using directed content analysis. For phase 2, EC cases from 2001–2015 were identified in SEER-Medicare. Location, provider type, and dates of symptom report and diagnosis were defined by claims data. The diagnostic interval was then calculated and step-wise multivariate modeling used to determine factors associated with time to diagnosis. Results: Phase 1 included 11 black women from 4 states (WA, LA, GA, CA), ages 47–70, stages 1––3 at diagnosis, for a total of 147 pages of transcribed interviews. Most were insured, with access to routine medical care. Common themes were a lack of knowledge of normal vs abnormal menopausal symptoms and silencing about bleeding among friends and family. The predominant interpretation of PMB was a resumption of normal menstruation, leading to significant delay in symptom disclosure. Reporting to an MD was largely driven by increased severity of bleeding or the onset of pain. Phase 2 included 3,363 EC cases, with 293 (8%) black women. The median diagnostic interval was 28 days (IQR: 8–110 days). After adjusting for age, region, gynecologic history and other presenting symptoms, provider differences were noted with shorter time for ER MDs (84%; P<.01) and PCPs (16%; P=.05) vs OBGYN. Characterization of bleeding as ‘abnormal’ rather than ‘postmenopausal’ prolonged time to diagnosis by 60% (P<.001). Black race was associated with a 2.4-fold increased diagnostic time interval (P=.017). Step-wise modeling showed that this association was explained by differences in diagnostic work-up: Compared to those with a biopsy within 7 days of presentation, women who had an ultrasound or no procedures had longer intervals (42% and 99%, respectively) to diagnosis (P<.001 for all). Conclusion: Among black women with access to medical care, there are modifiable factors that contribute to delays in diagnosis of EC both prior to and after symptom disclosure to a physician. This is the first study to identify targets for intervention to reduce the mortality rate in this high-risk group.

Bisphenol A affects larval growth and advances the onset of metamorphosis in Drosophila melanogaster

Exposure to Bisphenol A (BPA) has been reported to dysregulate endocrine pathways in a wide array of vertebrate species. The effects of BPA on invertebrate species are less well understood. We tested the effects of BPA on growth and development in Drosophila as these processes are governed by well-studied endocrine pathways. In this study, we tested the effects of three concentrations of BPA (0.1mg/L, 1mg/L or 10mg/L) and found a statistically significant increase in larval growth for the low dose treatment group (0.1mg/L), but not statistically significant for the high dose treatment group (10mg/L). BPA exposure resulted in an increased body size in treated animals at 48, 72 and 96h after egg laying (AEL). This finding reflects a non-monotonic dose-response that has been observed for an increasing number of endocrine disrupting compounds. The increase in growth rate found for all treatment groups was associated with a statistically significant increase in food intake observed at 72h AEL. Furthermore, we observed that the increased growth rate was coupled with an earlier onset of pupariation consistent with previously reported phenotypes resulting from increased activity of insulin/insulin growth factor signaling (IIS) in Drosophila. Since the timing of the onset of pupariation in Drosophila is controlled through the complex interaction of the IIS and the ecdysone signaling pathways, our findings suggest that BPA exerts its effects through disruption of endocrine signaling in Drosophila.

United States trends in patterns of care in clinical stage I testicular cancer: Results from the National Cancer Database (1998-2011)

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Background: There has been significant evolution in worldwide guidelines for management of clinical stage I (CS1) testicular cancer where active surveillance (AS) strategies are now considered a first choice, especially for patients with lower recurrence risk after orchiectomy. Conversely, local therapies for CS1 such as primary retroperitoneal lymphadenectomy (RPLND) in non-seminoma and regional radiation in seminoma are phasing out of recommendations. In the US, there have been no comprehensive efforts to measure uptake of guideline recommendations and modern patterns of care for early-stage testicular cancer. Methods: Access to the testicular cancer data set within the National Cancer Data Base (NCDB) was granted to Virginia Mason Medical Center (A SWOG affiliated cancer research program) for this retrospective cohort study. We identified all patients with CS1 testicular cancer between 1998 and 2011. Management options after orchiectomy such as adjuvant radiotherapy, adjuvant chemotherapy, RPLND, or AS were analyzed using cross tabulation and trend analysis. Results: Within the NCDB, of 75,902 patients with testicular cancer, 31,208 and 13,301 were diagnosed with CS1 seminoma and non-seminoma, respectively. For CS1 seminoma, AS use increased from 25.2% in 1998 to 55.8% in 2011. Similarly adjuvant chemotherapy use also increased (1.9 % to 16.7%). Conversely, use of adjuvant radiation decreased from 72.9% to 27.5%. For CS1 non-seminoma, AS remained the main treatment modality ranging between 58.8% and 66.2%. The use of adjuvant chemotherapy increased (28.3% in 2011) and the rate of primary RPLND constantly decreased down to 12.9% that same year. Interestingly, 50.3% of patients with CS1 non-seminoma and negative lympho-vascular invasion status had chemotherapy rather than AS. Trends analyses were statistically significant for all treatment modalities (p<0.05). Conclusions: Active surveillance as a management strategy has increased and is currently the most common treatment modality used for both CS1 seminoma and non-seminoma in the US. Regional therapies in CSI seminoma and non-seminoma are decreasing but persist even in patients with a low risk of recurrence.

Influence of social demographics and African-American race on outcomes in testicular cancer: Analysis of 75,902 patients in the National Cancer database

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Background: While there have been substantial advances in treatment and outcomes in testicular cancer, most of the data are derived from large institutionals or clinical trials. Testicular germ cell tumors are uncommon (8,000 new patients annually in US). The incidence among patients (pts) of African origins is extremely low. Most of the conclusions regarding outcomes are based on Caucasian pts from research institutions. Information about modern outcomes in non-Caucasian races is scant and little is known about the influence of various social demographic parameters on presentation patterns and survival. Using this population-based database available through the NCDB, we sought to better understand social and racial variations in outcomes. Methods: Within the NCDB, 75,902 testicular cancer pts were available for review. Tools available through the NCDB were utilized for analysis. Herein, we evaluated social demographics (insurance type, educational achievement, annual income, type of treating institution) and racial/ethnic characteristics as they pertained to stage at presentation and survival. Results: 75,902 pts were available from the timeframe of 1998 through 2011 for aggregation of social demographic features as well as racial/ethnic characteristics. Overall survival was available on 48573 pts through 2006. Racial-ethnic breakdown at presentation was 84.1% (n=63,867) Caucasian and African-American 2.7% (n=2,083). Overall, insurance type, education (% without high school degree), income (< $ 30000 to >$46,000) and type of treating hospital were analyzed using univariate and multivariate models. Full details will be presented. Conclusions: Unfavorable presentations and outcomes in testicular cancer are seen by race and social demographics. In depth analytics are being performed to characterize the variations as related to biological/genetic differences and/or differences in social demographics. In this very large cohort, the National Cancer database demonstrates a 2-fold risk increase in death in African American pts relative to Caucasian pts with similar stage at presentation.

Impact of chronic atrial fibrillation in patients with severe heart failure and indication for CRT: data of two registries with 711 patients (1999-2006 and 2007-6/2008)

AIMS

Atrial fibrillation (AF) is a relevant comorbidity in heart failure (HF) patients. In milestone cardiac resynchronization therapy (CRT) studies, patients with AF were excluded. We sought to investigate the influence of chronic atrial fibrillation (AF) on patients with CRT. AV node (AVN) ablation is frequently recommended. Converting AF to sinus rhythm (SR) is not a standard concept.

METHODS

A total of 584 consecutive patients with CRT devices were included in a single-center registry from 1999-2006 (retrospective registry) and 127/324 patients from 2007-06/2008 (prospective registry). The impact of persistent AF (group 1) on clinical and echocardiographic improvement compared with patients in SR (group 2) after 12 (6) months follow-up were analyzed. Re-establishing SR after initial cardioversion or need for AVN ablation was examined.

RESULTS

In the retrospective registry, 139 (24%) patients presented with AF (group 1) and 445 with SR (group 2). The groups differed in age, gender, and left atrium (LA) size but not in NYHA class, ejection fraction (EF), left ventricular end-diastolic dimension (LVEDD), B-type natriuretic peptide (BNP) levels, QRS width, and underlying disease. After 1 year, CRT improvement of NYHA class and EF was similar with higher mortality in group 1 (12% vs. 7%; OR 1.80; 95% confidence interval 0.95-3.4). The AF group presented with SR in 33/82 (40%) patients and 11% needed AVN ablation. The prospective data showed 27 (21%) patients in AF with conversion to SR in 41% after 6 months.

CONCLUSION

Patients with severe HF and chronic AF had a comparable improvement with CRT as those in SR. CRT is a successful treatment option in patients with chronic AF offering the potential to restore SR in a significant number of patients.

A new approach to overcome natural cholesterol interference during simultaneous determination of two stable isotope-enriched cholesterol tracers in human plasma

We have developed a validated gas chromatography/mass spectrometry (GC/MS) method with two labelled cholesterol tracers, i.e. (2)H(4) ([2H4]-Chol) and (2)H(7) ([2H7]-Chol) enriched moieties, with a new way of calculating the abundance of labelled cholesterol in plasma without natural cholesterol interference. The isotopomers of the analytes could interfere during analysis. Elimination of these interferences can be performed by the blank or mathematical subtraction method. Validation was performed with the two interference elimination methods. For both methods, linearity was obtained in the range 5 x 10(-4) to 10(-2) mM for both labelled cholesterol moieties. In the same range, repeatability and reproducibility were less than 6.5% and 7.5% for [2H4]-Chol and [2H7]-Chol, respectively. Accuracy was about 100% and recoveries always included 100% for the two labelled cholesterols. We demonstrate that measurement of blank plasma is not necessary when using the validated abundance isotope calculation method. This saves time, reagent and samples. This calculation strategy can be extrapolated to comparable tracer approaches.

Pediatric renal transplantation: a single center experience over 14 years

Between 1989 and 2003, 100 transplants were performed in 96 patients at the pediatric nephrology unit of the Calvo Mackenna Children's Hospital. Mean age 10.9 +/- 3.9 yr (1-17.6), 30% from LD. Donors were younger than 5 yr in five patients and all recipients received an 'en bloc' graft. Original disease was hypo/dysplasia 27%, reflux nephropathy 22 and 17% chronic glomerulonephritis. The immunosuppressive protocol during the first period (n = 56, 1989-2000): Cyclosporine, steroids and azathioprine, and during the second period (n = 44, 2001-2003): FK, steroids, MMF and anti-CD25 antibody (mAbs). AR was reported in 22 patients, 11% in LD, 31% in DD (p < 0.01). The AR rate decreased from 40 to 8% after anti-CD25 monoclonal induction. Patient actuarial survival rate at 1, 3 and 5 yr was 100% for LD and 96% for DD. The overall actuarial graft survival at 1,3, and 5 yr was 96.7, 96.7 and 71% for LD and 89, 76 and 73% for DD donors. Graft survival rate improved from the first period (1989-2000) to the second period (2001-2003; p = 0.05). No difference in graft survival rate with HLA-A,B,DR matching was found. Graft survival rate was better when cold ischemia time was <24 h (p < 0.01). CMV infections increased from 19 to 40% when MMF and anti-CD25 Ab were introduced (p < 0.01). The height/age Z score at 1, 3 and 5 yr post-transplant was -2.2, -2.1, -2.2, respectively, for children older than 7 yr and -1.8, -1.9, -2.1 for those transplanted younger than 7 yr of age who were switched to alternate day steroids (p < 0.01). The cause of graft lost was: chronic rejection eight, non-adherence four, AR four and vascular thrombosis two. The cause of death in two patients was fungus septicemia and accelerated rejection. Pediatric renal transplantation can be performed in our group with acceptable morbidity, low mortality and graft survival rates similar to other reports in North America and Western Europe. Graft survival rate improved with newer immunosuppression and greater experience at the center. Management of non-adherence and chronic rejection remain the major challenges.

Developing a genetic system in Deinococcus radiodurans for analyzing mutations

We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the beta-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif(r) system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced >250 mutations leading to Rif(r) in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N'-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.

Mutagenicity of the cytidine analog zebularine in Escherichia coli

We have examined the mutagenic properties of zebularine, a cytidine analog lacking the amino group at C-4 that has potential use in chemotherapy. Because the hydrate is a strong inhibitor of cytidine deaminase, its use can enhance the potency of other cytosine based compounds such as 5-azacytidine (5AzaC) and cytosine arabinoside (ara-C) that are inactivated by cytidine deaminase. Using the newly developed rpoB/Rifr system in Escherichia coli, we examined base substitution mutations caused by zebularine in the chromosomal rpoB gene. Zebularine is a potent mutagen that causes mainly G : C --> A : T transitions and favors certain hotspots. Mutations are not specific to the rpoB gene, since there is also a strong induction of mutations in the thyA gene. In the absence of mismatch repair, zebularine induces both base substitutions and frame shifts at rates well above those seen in wild-type strains treated with zebularine or in mismatch repair deficient strains without treatment. The nature of these induced mutations indicates that zebularine is stimulating the induction of increased replication errors, in addition to the targeted G : C --> A : T mutations, and that these errors are normally repaired by the mismatch repair system.

Polymerases leave fingerprints: analysis of the mutational spectrum in Escherichia coli rpoB to assess the role of polymerase IV in spontaneous mutation

We compared the distribution of mutations in rpoB that lead to rifampin resistance in strains with differing levels of polymerase IV (Pol IV), including strains with deletions of the Pol IV-encoding dinB gene, strains with a chromosomal copy of dinB, strains with the F'128 plasmid, and strains with plasmid amplification of either the dinB operon (dinB-yafNOP) or the dinB gene alone. This analysis identifies several hot spots specific to Pol IV which are virtually absent from the normal spontaneous spectrum, indicating that Pol IV does not contribute significantly to mutations occurring during exponential growth in liquid culture.

Identification of mutator genes and mutational pathways in Escherichia coli using a multicopy cloning approach

We searched for genes that create mutator phenotypes when put on to a multicopy plasmid in Escherichia coli. In many cases, this will result in overexpression of the gene in question. We constructed a random shotgun library with E. coli genomic fragments between 3 and 5 kbp in length on a multicopy plasmid vector that was transformed into E. coli to screen for frameshift mutators. We identified a total of 115 independent genomic fragments that covered 17 regions on the E. coli chromosome. Further studies identified 12 genes not previously known as causing mutator phenotypes when overproduced. A striking finding is that overproduction of the multidrug resistance transcription regulator, EmrR, results in a large increase in frameshift and base substitution mutagenesis. This suggests a link between multidrug resistance and mutagenesis. Other identified genes include those encoding DNA helicases (UvrD, RecG, RecQ), truncated forms of the DNA mismatch repair protein (MutS) and a primosomal component (DnaT), a negative modulator of initiation of replication/GATC-binding protein (SeqA), a stationary phase regulator AppY, a transcriptional regulator PaaX and three putative open reading frames, ycgW, yfjY and yjiD, encoding hypothetical proteins. In addition, we found three genes encoding proteins that were previously known to cause mutator effects under overexpression conditions: error-prone polymerase IV (DinB), DNA methylase (Dam) and sigma S factor (RpoS). This genomic strategy offers an approach to identify novel mutator effects resulting from the multicopy cloning (MCC) of specific genes and therefore complementing the conventional gene inactivation approach to finding mutators.

Developing a Genetic System in Deinococcus radiodurans for Analyzing Mutations

We have applied a genetic system for analyzing mutations in Escherichia coli to Deinococcus radiodurans, an extremeophile with an astonishingly high resistance to UV- and ionizing-radiation-induced mutagenesis. Taking advantage of the conservation of the β-subunit of RNA polymerase among most prokaryotes, we derived again in D. radiodurans the rpoB/Rif r system that we developed in E. coli to monitor base substitutions, defining 33 base change substitutions at 22 different base pairs. We sequenced &gt;250 mutations leading to Rif r in D. radiodurans derived spontaneously in wild-type and uvrD (mismatch-repair-deficient) backgrounds and after treatment with N-methyl-N′-nitro-N-nitrosoguanidine (NTG) and 5-azacytidine (5AZ). The specificities of NTG and 5AZ in D. radiodurans are the same as those found for E. coli and other organisms. There are prominent base substitution hotspots in rpoB in both D. radiodurans and E. coli. In several cases these are at different points in each organism, even though the DNA sequences surrounding the hotspots and their corresponding sites are very similar in both D. radiodurans and E. coli. In one case the hotspots occur at the same site in both organisms.

Loss of 9p21 is embedded in a complex but consistent pattern of genomic imbalances in oral squamous cell carcinomas

35 oral squamous cell carcinomas examined previously by comparative genomic hybridization (CGH) exhibited 5 up to 47 copy number alterations (CNAs). 13 of those cases showed a loss of parts of the short arm of chromosome 9, band p21 being affected in all of these cases. A highly complex but strikingly consistent pattern of genomic imbalances with an average 31.5 CNAs per tumor was associated with this deletion, and gains clearly dominated over losses of genomic material. Comparable patterns, however, could also be found in tumors with a high number of CNAs (24 CNAs) but without the deletion. Low numbers of imbalances were accompanied by low consistency of the CNA patterns. None of these latter cases showed the deletion 9p21. 66.7% of the dim(9p21)-positive tumors were of class pT4 (vs. 22% in dim(9p21)-negative cases), 77% of stage III or IV (vs. 47% in the group without the deletion), but only 8% of the dim(9p21)-positive tumors were classified as grade 3 (vs. 41% in the negative group). Other clinicopathologic features like prevalence of relapse, or survival time could not be as clearly associated with the deletion. For instance, short relapse-free survival was clearly associated with a high number of CNAs, rather independent of presence or absence of dim(9p21) in the affected tumor. From these findings it is concluded that previously found associations of 9p21 deletion with clinical parameters can reasonably be estimated only in the context of the pattern and complexity of the genomic imbalances accompanying this chromosomal loss in the examined tumors.