Josephine Kang

Extensive repetitive DNA facilitates prokaryotic genome plasticity

Prokaryotic genomes are substantially diverse, even when from closely related species, with the resulting phenotypic diversity representing a repertoire of adaptations to specific constraints. Within the microbial population, genome content may not be fixed, as changing selective forces favor particular phenotypes; however, organisms well adapted to particular niches may have evolved mechanisms to facilitate such plasticity. The highly diverse Helicobacter pylori is a model for studying genome plasticity in the colonization of individual hosts. For H. pylori, neither point mutation, nor intergenic recombination requiring the presence of multiple colonizing strains, is sufficient to fully explain the observed diversity. Here we demonstrate that H. pylori has extensive, nonrandomly distributed repetitive chromosomal sequences, and that recombination between identical repeats contributes to the variation within individual hosts. That H. pylori is representative of prokaryotes, especially those with smaller (<2 megabases) genomes, that have similarly extensive direct repeats, suggests that recombination between such direct DNA repeats is a widely conserved mechanism to promote genome diversification.

Stereotactic body radiotherapy with or without external beam radiation as treatment for organ confined high-risk prostate carcinoma: a six year study

BackgroundStereotactic Body Radiotherapy (SBRT) has excellent control rates for low- and intermediate-risk prostate carcinoma.The role of SBRT for high-risk disease remains less studied. We present long-term results on a cohort of patients with NCCN-defined high-risk disease treated with SBRT.MethodsWe retrospectively studied 97 patients treated as part of prospective trial from 2006–2010 with SBRT alone (n = 52) to dose of 35–36.25 Gy in 5 fractions, or pelvic radiation to 45 Gy followed by SBRT boost of 19–21 Gy in 3 fractions (n = 45). 46 patients received Androgen Deprivation Therapy. Quality of life and bladder/bowel toxicity was assessed using the Expanded Prostate Index Composite (EPIC) and RTOG toxicity scale.ResultsMedian followup was 60 months. 6-year biochemical disease-free survival (bDFS) was 69%. On multivariate analysis, only PSA remained significant (P < 0.01) for bDFS. Overall toxicity was mild, with 5% Grade 2–3 urinary and 7% Grade 2 bowel toxicity. Use of pelvic radiotherapy was associated with significantly higher bowel toxicity (P = .001). EPIC scores declined for the first six months and then returned towards baseline.ConclusionsSBRT appears to be a safe and effective treatment for high-risk prostate carcinoma. Our data suggests that SBRT alone may be the optimal approach. Further followup and additional studies is required to corroborate our results.

Current clinical trials testing the combination of immunotherapy with radiotherapy.

Increasing evidence demonstrates that radiation acts as an immune stimulus, recruiting immune mediators that enable anti-tumor responses within and outside the radiation field. There has been a rapid expansion in the number of clinical trials harnessing radiation to enhance antitumor immunity. If positive, results of these trials will lead to a paradigm shift in the use of radiotherapy. In this review, we discuss the rationale for trials combining radiation with various immunotherapies, provide an update of recent clinical trial results and highlight trials currently in progress. We also address issues pertaining to the optimal incorporation of immunotherapy with radiation, including sequencing of treatment, radiation dosing and evaluation of clinical trial endpoints.

Bacterial populations as perfect gases: genomic integrity and diversification tensions in Helicobacter pylori.

Microorganisms that persist in single hosts face particular challenges. Helicobacter pylori, an obligate bacterial parasite of the human stomach, has evolved a lifestyle that features interstrain competition and intraspecies cooperation, both of which involve horizontal gene transfer. Microbial species must maintain genomic integrity, yet H. pylori has evolved a complex nonlinear system for diversification that exists in dynamic tension with the mechanisms for ensuring fidelity. Here, we review these tensions and propose that they create a dynamic pool of genetic variants that is sufficiently genetically diverse to allow H. pylori to occupy all of the potential niches in the stomach.

Structural and Functional Divergence of MutS2 from Bacterial MutS1 and Eukaryotic MSH4-MSH5 Homologs

MutS homologs, identified in nearly all bacteria and eukaryotes, include the bacterial proteins MutS1 and MutS2 and the eukaryotic MutS homologs 1 to 7, and they often are involved in recognition and repair of mismatched bases and small insertion/deletions, thereby limiting illegitimate recombination and spontaneous mutation. To explore the relationship of MutS2 to other MutS homologs, we examined conserved protein domains. Fundamental differences in structure between MutS2 and other MutS homologs suggest that MutS1 and MutS2 diverged early during evolution, with all eukaryotic homologs arising from a MutS1 ancestor. Data from MutS1 crystal structures, biochemical results from MutS2 analyses, and our phylogenetic studies suggest that MutS2 has functions distinct from other members of the MutS family. A mutS2 mutant was constructed in Helicobacter pylori, which lacks mutS1 and mismatch repair genes mutL and mutH. We show that MutS2 plays no role in mismatch or recombinational repair or deletion between direct DNA repeats. In contrast, MutS2 plays a significant role in limiting intergenomic recombination across a range of donor DNA tested. This phenotypic analysis is consistent with the phylogenetic and biochemical data suggesting that MutS1 and MutS2 have divergent functions.

Stereotactic body radiotherapy as treatment for organ confined low- and intermediate-risk prostate carcinoma, a 7-year study.

Objectives: Stereotactic body radiation therapy (SBRT) takes advantage of the prostate’s low α/β ratio to deliver a large radiation dose in few fractions. Initial studies on small groups of low-risk patients support SBRT’s potential for clinical efficacy while limiting treatment-related morbidity and maintained quality of life. This prospective study expands upon prior studies to further evaluate SBRT efficacy for a large patient population with organ confined, low- and intermediate-risk prostate cancer patients. Methods: Four hundred seventy-seven patients with prostate cancer received CyberKnife SBRT. The median age was 68.6 years and the median PSA was 5.3 ng/mL. Three hundred twenty-four patients were low-risk (PSA <10 ng/mL and Gleason <7), 153 were intermediate-risk (PSA 10–20 ng/mL or Gleason = 7). Androgen deprivation therapy was administered to 51 patients for up to 6 months. One hundred fifty-four patients received 35 Gy delivered in five daily fractions; the remaining patients received a total dose of 36.25 Gy in five daily fractions. Biochemical failure was assessed using the phoenix criterion. Results: Median follow-up was 72 months. The median PSA at 7 years was 0.11 ng/mL. Biochemical failures occurred for 11 low-risk patients (2 locally), 14 intermediate-risk patients (3 locally). The actuarial 7-year freedom from biochemical failure was 95.6 and 89.6% for low- and intermediate-risk groups, respectively (p < 0.012). Among patients with intermediate-risk disease, those considered to have low intermediate-risk (Gleason 6 with PSA >10, or Gleason 3 + 4 with PSA <10; n = 106) had a significantly higher bDFS than patients with high intermediate-risk (Gleason 3 + 4 with PSA 10–20 or Gleason 4 + 3; n = 47), with bDFS of 93.5 vs. 79.3%, respectively. For the low-risk and low intermediate-risk groups, there was no difference in median PSA nadir or biochemical disease control between doses of 35 and 36.25 Gy. Conclusion: CyberKnife SBRT produces excellent biochemical control rates. Median PSA levels compare favorably with other radiation modalities and strongly suggest durability of response. These results also strongly suggest that 35 Gy is as effective as 36.25 Gy for low- and intermediate-risk patients.

Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation

Helicobacter pylori, bacteria that colonize the human gastric mucosa, are naturally competent for transformation by exogenous DNA, and show a panmic‐tic population structure. To understand the mechanisms involved in its horizontal gene transfer, we sought to define the interval required from exposure to substrate DNA until DNA uptake and expression of a selectable phenotype, as well as the relationship of transforming fragment length, concentration, homol‐ogy, symmetry, and strandedness, to the transformation frequency. We provide evidence that natural transformation in H. pylori differs in efficiency among wild‐type strains but is saturable and varies with substrate DNA length, symmetry, strandedness, and species origin. We show that H. pylori cells can be transformed within one minute of contact with DNA, by DNA fragments as small as 50 bp, and as few as 5 bp on one flank of a selectable single nucleotide mutation is sufficient substrate for recombination of a transforming fragment, and that double‐stranded DNA is the preferred (1000‐fold > single‐stranded) substrate. The high efficiency of double‐stranded DNA as transformation substrate, in conjunction with strain‐specific restriction endonucle‐ases suggests a model of short‐fragment recombination favoring closest relatives, consistent with the observed H. pylori population biology.—Levine S. M., Lin, E. A., Emara, W., Kang, J., DiBenedetto, M., Ando, T., Falush, D., Blaser M. J. Plastic cells and populations: DNA substrate characteristics in Helicobacter pylori transformation define a flexible but conservative system for genomic variation. FASEB J. 21, 3458–3467 (2007)

Quality of Life and Toxicity after SBRT for Organ-Confined Prostate Cancer, a 7-Year Study

Objectives: Stereotactic body radiation therapy (SBRT) yields excellent disease control for low- and intermediate-risk prostate cancer by delivering high doses of radiation in a small number of fractions. Our report presents a 7-year update on treatment toxicity and quality of life (QOL) from 515 patients treated with prostate SBRT. Methods: From 2006 to 2009, 515 patients with clinically localized, low-, intermediate-, and high-risk prostate cancer were treated with SBRT using Cyberknife technology. Treatment consisted of 35–36.25 Gy in 5 fractions. Seventy-two patients received hormone therapy. Toxicity was assessed at each follow-up visit using the expanded prostate cancer index composite (EPIC) questionnaire and the radiation therapy oncology group urinary and rectal toxicity scale. Results: Median follow-up was 72 months. The actuarial 7-year freedom from biochemical failure was 95.8, 89.3, and 68.5% for low-, intermediate-, and high-risk groups, respectively (p < 0.001). No patients experienced acute Grade 3 or 4 acute complications. Fewer than 5% of patients had any acute Grade 2 urinary or rectal toxicity. Late toxicity was low, with Grade 2 rectal and urinary toxicity of 4 and 9.1%, respectively, and Grade 3 urinary toxicity of 1.7%. Mean EPIC urinary and bowel QOL declined at 1 month post-treatment, returned to baseline by 2 years and remained stable thereafter. EPIC sexual QOL declined by 23% at 6–12 months and remained stable afterwards. Of patients potent at baseline evaluation, 67% remained potent at last follow-up. Conclusion: This study suggests that SBRT, when administered to doses of 35–36.25 Gy, is efficacious and safe. With long-term follow-up in our large patient cohort, we continue to find low rates of late toxicity and excellent rates of biochemical control.

Antimutator Role of the DNA Glycosylase mutY Gene in Helicobacter pylori

Helicobacter pylori has a highly variable genome with ongoing diversification via inter- and intragenomic recombination and spontaneous mutation. DNA repair genes modulating mutation and recombination rates that influence diversification have not been well characterized for H. pylori. To examine the role of putative base excision repair ung and mutY glycosylase and xthA apurinic/apyrimidinic endonuclease genes in H. pylori, mutants of each were constructed in strain JP26 by allelic exchange. Spontaneous mutation frequencies of JP26 mutY mutants, assessed by rifampin resistance, were consistently higher (26-fold) than that of the wild type, whereas the ung and xthA mutants showed smaller increases. In trans complementation of the JP26 mutY mutant restored spontaneous mutation frequencies to wild-type levels. In cross-species studies, H. pylori mutY complemented an Escherichia coli mutY mutant and vice versa. In contrast, the ung and mutY mutants did not show higher frequencies of intergenomic recombination or greater sensitivity to UV-induced DNA damage than the wild type. The H. pylori mutY open reading frame contains an eight-adenine homonucleotide tract; we provide evidence that this is subject to slipped-strand mispairing, leading to frameshifts that eliminate gene function. Our findings indicate that H. pylori possesses phase-variable base excision repair, consistent with a tension between repair and mutation.

Effect of Host Species on RecG Phenotypes in Helicobacter pylori and Escherichia coli

Recombination is a fundamental mechanism for the generation of genetic variation. Helicobacter pylori strains have different frequencies of intragenomic recombination, arising from deletions and duplications between DNA repeat sequences, as well as intergenomic recombination, facilitated by their natural competence. We identified a gene, hp1523, that influences recombination frequencies in this highly diverse bacterium and demonstrate its importance in maintaining genomic integrity by limiting recombination events. HP1523 shows homology to RecG, an ATP-dependent helicase that in Escherichia coli allows repair of damaged replication forks to proceed without recourse to potentially mutagenic recombination. Cross-species studies done show that hp1523 can complement E. coli recG mutants in trans to the same extent as E. coli recG can, indicating that hp1523 has recG function. The E. coli recG gene only partially complements the hp1523 mutation in H. pylori. Unlike other recG homologs, hp1523 is not involved in DNA repair in H. pylori, although it has the ability to repair DNA when expressed in E. coli. Therefore, host context appears critical in defining the function of recG. The fact that in E. coli recG phenotypes are not constant in other species indicates the diverse roles for conserved recombination genes in prokaryotic evolution.