Long-read sequencing for fast and robust identification of correct genome-edited alleles: PCR-based and Cas9 capture methods

BACKGROUND

Recent developments in CRISPR/Cas9 genome-editing tools have facilitated the introduction of precise alleles, including genetic intervals spanning several kilobases, directly into the embryo. However, the introduction of donor templates, via homology directed repair, can be erroneous or incomplete and these techniques often produce mosaic founder animals. Thus, newly generated alleles must be verified at the sequence level across the targeted locus. Screening for the presence of the desired mutant allele using traditional sequencing methods can be challenging due to the size of the interval to be sequenced, together with the mosaic nature of founders.

METHODOLOGY/PRINCIPAL FINDINGS

In order to help disentangle the genetic complexity of these animals, we tested the application of Oxford Nanopore Technologies long-read sequencing at the targeted locus and found that the achievable depth of sequencing is sufficient to offset the sequencing error rate associated with the technology used to validate targeted regions of interest. We have assembled an analysis workflow that facilitates interrogating the entire length of a targeted segment in a single read, to confirm that the intended mutant sequence is present in both heterozygous animals and mosaic founders. We used this workflow to compare the output of PCR-based and Cas9 capture-based targeted sequencing for validation of edited alleles.

CONCLUSION

Targeted long-read sequencing supports in-depth characterisation of all experimental models that aim to produce knock-in or conditional alleles, including those that contain a mix of genome-edited alleles. PCR- or Cas9 capture-based modalities bring different advantages to the analysis.

Interlaboratory evaluation of Mucorales PCR assays for testing serum specimens: A study by the fungal PCR Initiative and the Modimucor study group

Interlaboratory evaluations of Mucorales qPCR assays were developed to assess the reproducibility and performance of methods currently used. The participants comprised 12 laboratories from French university hospitals (nine of them participating in the Modimucor study) and 11 laboratories participating in the Fungal PCR Initiative. For panel 1, three sera were each spiked with DNA from three different species (Rhizomucor pusillus, Lichtheimia corymbifera, Rhizopus oryzae). For panel 2, six sera with three concentrations of R. pusillus and L. corymbifera (1, 10, and 100 genomes/ml) were prepared. Each panel included a blind negative-control serum. A form was distributed with each panel to collect results and required technical information, including DNA extraction method, sample volume used, DNA elution volume, qPCR method, qPCR template input volume, qPCR total reaction volume, qPCR platform, and qPCR reagents used. For panel 1, assessing 18 different protocols, qualitative results (positive or negative) were correct in 97% of cases (70/72). A very low interlaboratory variability in Cq values (SD = 1.89 cycles) were observed. For panel 2 assessing 26 different protocols, the detection rates were high (77-100%) for 5/6 of spiked serum. There was a significant association between the qPCR platform and performance. However, certain technical steps and optimal combinations of factors may also impact performance. The good reproducibility and performance demonstrated in this study support the use of Mucorales qPCR as part of the diagnostic strategy for mucormycosis.

Universal Southern blot protocol with cold or radioactive probes for the validation of alleles obtained by homologous recombination

The widespread availability of recombineered vectors and gene targeted embryonic stem cells from large-scale repositories facilitates the generation of mouse models for functional genetic studies. Southern blotting validates the structure of these targeted alleles produced by homologous recombination, as well as indicating any additional integrations of the vector into the genome. Traditionally this technique employs radioactively-labelled probes; however, there are many laboratories that are restricted in their use of radioactivity. Here, we present a widely applicable protocol for Southern blot analysis using cold probes and alternative procedures employing radioactive probes. Furthermore, the probes are designed to recognise standardised regions of gene-targeting cassettes and so represent universally applicable reagents for assessing allelic integrity.

Application of long single-stranded DNA donors in genome editing: generation and validation of mouse mutants

Background

Recent advances in clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated protein 9 (Cas9) genome editing have led to the use of long single-stranded DNA (lssDNA) molecules for generating conditional mutations. However, there is still limited available data on the efficiency and reliability of this method.

Results

We generated conditional mouse alleles using lssDNA donor templates and performed extensive characterization of the resulting mutations. We observed that the use of lssDNA molecules as donors efficiently yielded founders bearing the conditional allele, with seven out of nine projects giving rise to modified alleles. However, rearranged alleles including nucleotide changes, indels, local rearrangements and additional integrations were also frequently generated by this method. Specifically, we found that alleles containing unexpected point mutations were found in three of the nine projects analyzed. Alleles originating from illegitimate repairs or partial integration of the donor were detected in eight projects. Furthermore, additional integrations of donor molecules were identified in four out of the seven projects analyzed by copy counting. This highlighted the requirement for a thorough allele validation by polymerase chain reaction, sequencing and copy counting of the mice generated through this method. We also demonstrated the feasibility of using lssDNA donors to generate thus far problematic point mutations distant from active CRISPR cutting sites by targeting two distinct genes (Gckr and Rims1). We propose a strategy to perform extensive quality control and validation of both types of mouse models generated using lssDNA donors.

Conclusion

lssDNA donors reproducibly generate conditional alleles and can be used to introduce point mutations away from CRISPR/Cas9 cutting sites in mice. However, our work demonstrates that thorough quality control of new models is essential prior to reliably experimenting with mice generated by this method. These advances in genome editing techniques shift the challenge of mutagenesis from generation to the validation of new mutant models.

Electronic supplementary material

The online version of this article (10.1186/s12915-018-0530-7) contains supplementary material, which is available to authorized users.

Posterior urethral injuries associated with motorcycle accidents and pelvic trauma in adolescents: analysis of urethral lesions occurring prior to a bony fracture using a computerized finite-element model

Adolescent males involved in motorcycle accidents are particularly at risk for pelvic injury, which may provoke a posterior urethral injury. The aim of this study was to develop a model to analyze the association between injuries and fractures of the pelvic ring and the risk of posterior urethral injury.

METHOD

Based on experience with traffic accident modeling, a computerized finite-element model was extrapolated from a computerized tomography scan of a 15-year-old boy. The anatomic structures concerned in urethral and pelvic ring trauma were isolated, rendered in 3D and given biomechanical properties. The model was verified according to available experiments on pelvic ring trauma.

RESULTS

To apply the model, we recreated three impact mechanisms on the pelvic ring: lateral impact, antero-posterior impact and a real car‒motorcycle accident situation (postero-lateral impact). In all three situations, stretching of the posterior urethra was identified prior to bony fracture visualization.

CONCLUSION

Application of this model allowed us to analyze precisely the link between trauma of the pelvic ring and lesions of the posterior urethra. The results should help to establish guidelines for urethral catheterization in male adolescents in cases of pelvic trauma, even when no bony fracture is present, in order to prevent iatrogenic worsening of a misdiagnosed posterior urethral trauma.

Effects of growth hormone deficiency on body composition and biomarkers of cardiovascular risk after definitive therapy for acromegaly

BACKGROUND

Both growth hormone (GH) excess and GH deficiency are associated with abnormalities in body composition and biomarkers of cardiovascular risk in patients with pituitary disorders. However, the effects of developing GH deficiency after definitive treatment of acromegaly are largely unknown.

OBJECTIVE

To determine whether development of GH deficiency after definitive therapy for acromegaly is associated with increased visceral adiposity and biomarkers of cardiovascular risk compared with GH sufficiency after definitive therapy for acromegaly.

DESIGN

Cross-sectional.

PATIENTS

We studied three groups of subjects, all with a history of acromegaly (n = 76): subjects with subsequent GH deficiency (GHD; n = 31), subjects with subsequent GH sufficiency (GHS; n = 25) and subjects with active acromegaly (AA; n = 20). No study subjects were receiving somatostatin analogues, dopamine agonists or hGH.

MEASUREMENTS

Body composition (by DXA), abdominal adipose tissue depots (by cross-sectional CT), total body water (by bioimpedance analysis) and carotid intima-media thickness (IMT) were measured. Fasting morning serum was collected for high-sensitivity C-reactive protein (hsCRP), lipids and lipoprotein levels. An oral glucose tolerance test was performed, and homoeostasis model of assessment-insulin resistance (HOMA-IR) was calculated.

RESULTS

Abdominal visceral adipose tissue, total adipose tissue and total body fat were higher in subjects with GHD than GHS or AA (P < 0·05). Subcutaneous abdominal fat was higher, and fibrinogen and IMT were lower in GHD (but not GHS) than AA (P < 0·05). Patients with GHD had the highest hsCRP, followed by GHS, and hsCRP was lowest in AA (P < 0·05). Fasting glucose, 120-min glucose, fasting insulin, HOMA-IR and per cent total body water were lower in GHD and GHS than AA (P < 0·05). Triglycerides were higher in GHS than AA (P < 0·05). Lean body mass, mean arterial pressure, total cholesterol, HDL and LDL were comparable among groups.

CONCLUSIONS

Development of GHD after definitive treatment of acromegaly may adversely affect body composition and inflammatory biomarkers of cardiovascular risk but does not appear to adversely affect glucose homoeostasis, lipids and lipoproteins, or other cardiovascular risk markers.

Posterior urethral injuries associated with pelvic injuries in young adults: computerized finite element model creation and application to improve knowledge and prevention of these lesions

INTRODUCTION

Young adult males involved in motorcycle accidents are particularly at risk for posterior urethral injury whenever pelvic injury occurs. Posterior urethral injuries remain problematic because their diagnosis may be missed, and during the initial treatment response the urethral injury can be aggravated by urethral catheterization. Few anatomical and clinical tools exist that establish a correlation between injuries and fractures of the pelvic ring and the risk of posterior urethral injury.

METHOD

Based on experience with traffic accident modeling, a computerized finite element model was conceived integrating the specific anatomic structures concerned. This model was extrapolated from a CAT scan of a young adult. The anatomic structures concerned in urethral and pelvic ring trauma (PRT) were isolated, placed in 3D and given biomechanical properties. The model was verified according to available experiments on PRT.

RESULTS

To apply the model, we recreated a lateral impact mechanism on the pelvic ring. Stretching between the prostatic and membranous portions of the urethra (before and after visualization of a pelvic fracture) as well as timing of injury was studied.

CONCLUSION

The model's application permitted us to analyze precisely the link between lateral impact trauma of the pelvic ring and lesions of the posterior urethra and to identify an urethra stretching prior to visualization of a pelvic fracture. Utilization of the model with other mechanisms of injury should allow for better comprehension of this associated trauma, improved prevention, iatrogenic aggravation of, and care for, these serious injuries.

Caveolin-1 modulates TGF-β1 signaling in cardiac remodeling

The cardiac response to myocardial injury includes fibrotic and hypertrophic processes and a key mediator in this response is transforming growth factor-β1 (TGF-β1). Caveolin-1 (cav1), the main structural protein of caveolae, is an inhibitor of the TGF-β1 signaling pathway. To examine the role of cav1 in cardiac repair, cav1 deficient (Cav1(-/-)) and wild type (WT) mice were subjected to cryoinjury of the left ventricle (LV). At baseline the two groups exhibited no inflammation, similar collagen content, and similar cardiac function. After injury, Cav1(-/-) animals displayed enhanced TGF-β1 signaling, as reflected by a 3-fold increase in the activation of the Smad2-dependent pathway and more widespread collagen deposition in the heart. Qualitative and quantitative analyses indicated that collagen deposition peaked in the WT LV 14days after injury, accompanied by increased mRNA abundance for procol1a2 (2-fold) and procol3a1 (3-fold). Collagen deposition was further enhanced in Cav1(-/-) mice, which was accompanied by reduced expression of matrix metalloproteinases MMP-8 (3-fold) and -13 mRNA (2-fold). The levels of expression of inflammatory markers of acute phase were similar between the strains However, macrophage clearance in the damaged region was delayed in Cav1(-/-) mice. We observed a 4-fold decrease in collagen deposition in Cav1(-/-) mice injected with a cav1 scaffolding domain peptide (CSD) and a 2-fold decrease in WT mice treated with the CSD. We conclude that cav1 has a direct role in reducing TGF-β1 signaling and as such might be an appropriate target for therapies to influence cardiac remodeling.

Endophthalmitis as primary clinical manifestation of fatal fusariosis in an allogeneic stem cell recipient

The occurrence of infections due to previously rare opportunistic pathogens is increasing despite the use of novel treatment strategies for immunocompromised patients. Here, we report the case of a patient presenting with fever, muscle pain, and bilateral endophthalmitis after allogeneic hematopoietic stem cell transplantation. Fusarium solani was isolated from peripheral blood samples and identified as the cause of gradual bilateral vision loss, despite appropriate antifungal prophylaxis, and therapy including vitrectomy and intraocular instillation of antifungal agents. The patient became comatose; basal meningitis involving both optic nerves was suspected based on magnetic resonance tomography. The patient died 8 days later due to septic multi-organ failure. Autopsy revealed that both kidneys, but no other organs, were infiltrated by Fusarium. No fungus was found in cerebral tissues or cerebrospinal fluid. Our case demonstrates some of the typical clinical features of systemic fusariosis and its potentially fatal outcome. The clinical observations reported here may help clinicians caring for immunocompromised patients to accelerate diagnosis and initiate treatment early at the onset of this fatal complication, and highlight the urgent need for interdisciplinary management of invasive fusariosis.

Dynamics of extracellular release of Aspergillus fumigatus DNAand galactomannan during growth in blood and serum

Aspergillus fumigatus is the major cause of invasive aspergillosis (IA),a disease associated with high rates of morbidity and mortality in patientsundergoing treatment for haematological malignancies. This study investigated A. fumigatus growth in vitro and in a murine model of IA inorder to provide insights into the dynamics of extracellular DNA and galactomannan (GM)release and their relevance to early diagnosis of IA. Following inoculationof whole blood with 20 A. fumigatus conidia ml−1,DNA that corresponded to the inoculum could be detected by PCR but GM wasnot detected in plasma separated from the blood sample, indicating that thefungus did not grow in whole blood. The quantities of DNA detected by PCR,and GM, were proportional to the amount of fungal biomass present in vitro. Fungal DNA could be detected in the sera of mice experimentally infectedwith A. fumigatus with maximum detection in cyclophosphamide-treatedmice.

Investigation of promoter variations in dendritic cell-specific ICAM3-grabbing non-integrin (DC-SIGN) (CD209) and their relevance for human cytomegalovirus reactivation and disease after allogeneic stem-cell transplantation

Promoter variations in Toll-like receptor genes (n = 7) and genes encoding pathogen recognition and virus entry receptors (n = 7) were screened to detect any association with human cytomegalovirus (hCMV) reactivation and disease in patients following allogeneic stem-cell transplantation. Two single nucleotide polymorphisms (rs735240, G>A; rs2287886, C>T) in the promoter region of the dendritic cell-specific ICAM3-grabbing non-integrin (DC-SIGN) showed a significant association with an increased risk of development of hCMV reactivation and disease. Furthermore, these genetic markers influenced the expression levels of DC-SIGN on immature dendritic cells, as well as the infection efficiency of immature dendritic cells by hCMV, as determined by hCMV immediate-early antigen staining. Screening of patients following allogeneic stem-cell transplantation for the presence of these defined genetic polymorphisms might help to predict the individual risk of hCMV reactivation and disease.

Evaluation of the COBAS Amplicor HCMV Monitor for early detection and monitoring of human cytomegalovirus infection after allogeneic stem cell transplantation

Early diagnosis of human cytomegalovirus (HCMV) infection and the introduction of preemptive antiviral therapy have reduced HCMV-related mortality after allogeneic stem cell transplantation. A critical goal remains stratifying risk profiles and minimizing potential harm owing to antiviral overtreatment. We compared the commercially available standardized COBAS Amplicor CMV Monitor (CACM) to an in-house PCR assay, for the monitoring of HCMV infection. Seventy-two patients were surveyed by an in-house PCR of whole blood, quantitative viral load assessment by CACM and virus culture assays in a prospective and a retrospective study. A high concordance between CACM and PCR was documented. The viral load at onset correlated with the peak viral load (Spearman rank correlation R=0.634, P=0.0004). In patients developing HCMV disease, both viral loads were in trend higher (P=0.823, respectively P=0.053), and the viremic episodes longer (P=0.015), as compared to asymptomatically HCMV-infected patients. The serological pre-transplant status was the major risk factor for the development of HCMV disease, showing highest risk for seropositive patients receiving a seronegative graft, whereas donor type (related or unrelated) and graft type (bone marrow or peripheral blood mobilized stem cells) did not have an influence. HCMV infection proved to be a risk factor for the development of non-viral opportunistic infections (P=0.002).

Polymorphisms in genes of folate metabolism and effects of high-dose methotrexate in patients with primary central nervous system lymphoma

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Background: The antifolate methotrexate (MTX) is the single most effective agent in primary central nervous system lymphoma (PCNSL) when given intravenously in high doses. MTX inhibits 5,10-methylentetrahydrofolate reductase (MTHFR) as well as thymidylate synthase (TYMS) in target cells what eventually results in decreased DNA synthesis. Intracellular uptake of folates is mediated by the reduced folate carrier (RFC). Two common MTHFR single nucleotide polymorphisms (SNPs) affect enzyme activity: 677 C→T and 1298A→C. A 28 base pair (bp) tandemly repeated sequence in the TYMS enhancer region (5’-UTR) containing either 2 or 3 repeats alters enzyme activity as does a 6 bp deletion (del) polymorphism in the 3’-UTR of TYMS. An RFC SNP (80G→A) is known to influence folate and MTX transport. We hypothesized that these polymorphisms may be directly linked to toxicity in PCNSL patients receiving high-dose MTX. Methods: Genomic DNA was prospectively collected from patients (pts) who received high-dose (HD) MTX 4 g/m2 every 2 weeks after enrolment onto the German multicenter G-PCNSL-SG1 trial. Genotyping of the two MTHFR and the RFC SNPs was performed by melting point analysis using the Light Cycler technology. Genotyping of the TYMS 28bp polymorphism was performed by conventional PCR followed by agarose gel electrophoresis. The TYMS 6bp del polymorphism was analyzed by PCR, restriction enzyme digest and agarose gel electrophoresis. Response, hematologic (Hb, WBC, ANC, platelets) as well as cumulative incidence of non-hematologic toxicity (renal, pulmonary, mucositis) were assessed prospectively. Results: 123 pts are evaluvable for clinical parameters. Relative risk of any °III/IV toxicity was 26-fold higher for pts with 677TT when compared to CT or CC genotype (p = 0.009). °III/IV non-hematologic toxicity for TT was 10-fold higher than with CT or CC (p = 0.02). Significant differences for hematologic values were restricted to WBC and ANC and found to be associated with RFC 80 GG vs. AG/AA (p = 0.047). Conclusions: Pharmacogenetic studies may identify PCNSL pts who are at risk for severe hematologic and non-hematologic toxicity when treated with HD-MTX.

No significant financial relationships to disclose.

Familial renal glucosuria: SLC5A2 mutation analysis and evidence of salt-wasting

Familial renal glucosuria (FRG) is an inherited renal tubular disorder characterized by persistent isolated glucosuria in the absence of hyperglycemia. Mutations in the sodium/glucose co-transporter SGLT2 coding gene, SLC5A2, were recently found to be responsible for the disorder. Here, we report the molecular and phenotype study of five unrelated FRG families. Five patients were identified and their family members screened for glucosuria. SLC5A2 coding region of index cases was polymerase chain reaction amplified and sequenced. Five different mutations are reported, including four novel alleles. The IVS12+1G>A and p.A102V alleles were identified in homozygosity in index patients of two unrelated families. A proband from another family was compound heterozygous for the p.R132H and p.A219T mutations, and the heterozygous p.Q167fsX186 frameshift allele was the only mutation detected in the affected individual from an additional pedigree. For the remaining family no mutations were detected. The patient homozygous for the p.A102V mutation had glucosuria of 65.6 g/1.73 m(2)/24 h, evidence of renal sodium wasting, mild volume depletion, and raised basal plasma renin and serum aldosterone levels. Our findings confirm previous observations that in FRG, transmitted as a codominant trait with incomplete penetrance, most mutations are private. In the only patient with massive glucosuria in our cohort there was evidence evocative of renin-angiotensin aldosterone system activation by extracellular volume depletion induced by natriuresis. Definite proof of renin-angiotensin aldosterone system activation in FGR should rely on evaluation of additional patients with massive glucosuria.

Effects of testosterone replacement in androgen-deficient women with hypopituitarism: a randomized, double-blind, placebo-controlled study

CONTEXT

Hypopituitarism in women is characterized by profound androgen deficiency due to a loss of adrenal and/or ovarian function. The effects of testosterone replacement in this population have not been reported.

OBJECTIVE

The objective of the study was to determine whether physiologic testosterone replacement improves bone density, body composition, and/or neurobehavioral function in women with severe androgen deficiency secondary to hypopituitarism.

DESIGN

This was a 12-month randomized, placebo-controlled study.

SETTING

The study was conducted at a general clinical research center.

STUDY PARTICIPANTS

Fifty-one women of reproductive age with androgen deficiency due to hypopituitarism participated.

INTERVENTION

Physiologic testosterone administration using a patch that delivers 300 microg daily or placebo was administered.

MAIN OUTCOME MEASURES

Bone density, fat-free mass, and fat mass were measured by dual x-ray absorptiometry. Thigh muscle and abdominal cross-sectional area were measured by computed tomography scan. Mood, sexual function, quality of life, and cognitive function were assessed using self-administered questionnaires.

RESULTS

Mean free testosterone increased into the normal range during testosterone administration. Mean hip (P = 0.023) and radius (P = 0.007), but not posteroanterior spine, bone mineral density increased in the group receiving testosterone, compared with placebo, as did mean fat-free mass (P = 0.040) and thigh muscle area (P = 0.038), but there was no change in fat mass. Mood (P = 0.029) and sexual function (P = 0.044) improved, as did some aspects of quality of life, but not cognitive function. Testosterone at physiologic replacement levels was well tolerated, with few side effects.

CONCLUSIONS

This is the first randomized, double-blind, placebo-controlled study to show a positive effect of testosterone on bone density, body composition, and neurobehavioral function in women with severe androgen deficiency due to hypopituitarism.

Evaluation of the NucliSens CMV pp67 assay for detection and monitoring of human cytomegalovirus infection after allogeneic stem cell transplantation

Preemptive treatment based on the sensitive detection of CMV-DNA has helped to reduce HCMV-related mortality after allogeneic stem cell transplantation (SCT). Detection of active viral replication might help to better predict HCMV disease. In this study, 33 recipients at risk for HCMV infection after allogeneic SCT were prospectively monitored 1x/week for active HCMV infection by NASBA, whole blood DNA-PCR and virus culture assays. Preemptive antiviral therapy was initiated after the second positive PCR result, while NASBA results were not considered for clinical decision-making. Overall, a high agreement between PCR and NASBA on a per sample (85.3%) and per patient (87.9%) level was demonstrated. HCMV DNA titers in the blood were found to be higher in PCR(+)/NASBA(+) compared to PCR(+)/NASBA(-) samples (P < 0.01). None of the NASBA-negative patients developed HCMV disease. Sixteen of 18 patients receiving PCR-based preemptive therapy were also found NASBA positive. There was no difference between the assays for the time to the first positive test result. However, the time to the first negative test result upon initiation of antiviral therapy was significantly shorter for the NASBA assay (P = 0.002), indicating a high positive predictive value to assess the efficacy of antiviral therapy. Three patients developed late-onset HCMV disease, all of whom were found to be PCR and NASBA positive. In conclusion, the data presented clearly demonstrate the value of patient monitoring using the NASBA assay to early diagnose active HCMV infection and to assess the efficacy of antiviral therapy in high risk patients after allogeneic SCT. A prospective comparison of PCR-based vs NASBA-based preemptive therapy is ongoing.

Diagnosis of disseminated zygomycosis using a polymerase chain reaction assay

Invasive pulmonary zygomycosis is an uncommon opportunistic infection in patients with haematological malignancies. Clinical manifestations are in distinguishable from the more frequent invasive aspergillosis. Standard diagnostic methods like culture and microscopy from respiratory secretions have a low diagnostic sensitivity. A case in which proven invasive pulmonary zygomycosis was confirmed using a panfungal polymerase chain reaction assay in blood is presented. Since zygomycosis requires more aggressive treatment than aspergillosis (high-dose amphotericin B and surgical intervention), the polymerase chain reaction assay may improve the outcome of these often fatal infections by guiding the therapeutic approach through an early, non-invasive diagnosis.

Evaluation of the Murex CMV DNA Hybrid Capture assay (version 2.0) for early diagnosis of cytomegalovirus infection in recipients of an allogeneic stem cell transplant

Early diagnosis of CMV infection based on sensitive diagnostic assays has helped to reduce CMV-related mortality after allogeneic stem cell transplantation (SCT). In this study, the commercialized Murex CMV DNA Hybrid Capture assay (version 2.0) (HCS) was prospectively compared to an in-house CMV-DNA PCR assay from whole blood in patients after allogeneic stem cell transplantation. Overall, a high concordance between HCS and PCR was documented (kappa = 0.686; n = 385). The HCS assay was found to be as sensitive as the PCR indicating active CMV infection at a median of 35 and 34 days after transplantation, respectively. None of the HCS-negative patients developed CMV-related symptoms (negative predictive value 100%). Declining CMV DNA load in the blood was found to be an indicator for effective antiviral therapy, whereas persistence of a high viral load was associated with fatal CMV disease. In conclusion, the Hybrid Capture CMV DNA assay (v 2.0) allows early diagnosis of CMV infection after allogeneic SCT and assessment of the efficacy of antiviral therapy.

Nucleic acid sequence-based amplification of Aspergillus RNA in blood samples

Nucleic acid sequence-based amplification (NASBA), an isothermal amplification technique, was established and evaluated for the detection of Aspergillus RNA and compared with a previously published, well-defined real-time PCR assay amplifying a region of the Aspergillus 18S rRNA gene. NASBA showed a lower detection limit of 1 CFU and detected RNA from five different clinically relevant Aspergillus species, including Aspergillus fumigatus. All 77 blood samples tested by PCR and NASBA showed identical results in both assays. Results with the NASBA technique were obtained within 6 h. Thus, the NASBA technique provided a valuable tool for sensitive, specific, fast, and reliable detection of Aspergillus RNA with potential for routine diagnosis, including the possibility to test the viability of cells.

Practice parameters for the management of single brain metastasis

Object

In January 1998 the Guidelines and Outcomes Committee of the American Association of Neurological Surgeons (AANS) issued a charge for the development of evidence-based practice parameters focusing on the treatment of patients with single metastasis to the brain. The charge was imposed in response to the significant controversy surrounding questions relating to the optimal management strategies for patients with single brain metastasis.

Methods

A team consisting of physicians from the AANS, the American Academy of Neurology, and the American Association of Therapeutic Radiation Oncology convened and the literature was reviewed. Methodically drawing from the best of Class I, II, and III levels of available evidence, authors sought to determine how the literature addressed and disposed of the question of the optimal management for an adult with a known history of cancer and a single meta-static brain lesion. Framing the question in this specific manner allowed researchers to focus directly on treatment issues, without having to consider diagnostic issues.

Conclusions

The results of the evidence-based analysis demonstrated that there was insufficient information to establish standards of care. Data from the literature does, however, support a guideline stating that surgical resection accompanied by whole brain radiation therapy is associated with the best survival rate. Additional lower-quality evidence supports an option for management with radiosurgery.

Identification of rare Candida species and other yeasts by polymerase chain reaction and slot blot hybridization

Invasive candidiasis has become a major cause of morbidity and mortality in immunocompromised hosts. Here we describe a fast and reliable DNA extraction and PCR amplification method in combination with a slot blot hybridization assay. A genus-specific probe was designed that allowed to detect DNA from a broad range of Candida species and 3 other yeasts. In addition, species-specific oligonucleotides for emerging Candida and other yeast species allowed to identify DNA extracted from Candida lusitaniae, Candida humicola, Candida kefyr, Candida inconspicua, Candida solani, Malassezia furfur and Trichosporon cutaneum. A sensitivity of at least 10(1) CFU, corresponding to 100 fg of fungal DNA, was documented for all species-specific probes and the common Candida probe. In addition, the 18S rRNA genes of 7 yeast species (C. humicola, C. kefyr, C. solani, C. inconspicua, C. norvegensis, C. utilis and M. furfur) were completely sequenced. The sequencing primers described bind to highly conserved primer binding sites. Therefore, these primers would allow rapid cycle sequence of additional ribosomal genes throughout the whole kingdom of fungi.

Comparison between plasma and whole blood specimens for detection of Aspergillus DNA by PCR

Ninety-six plasma and whole blood specimens from nine selected patients were analyzed for the presence of Aspergillus DNA. Nineteen specimens from three patients with proven aspergillosis were PCR positive in both materials, whereas an additional 22 were PCR positive in whole blood only. All 36 samples from six patients without signs of aspergillosis were negative in both assays. We conclude that although plasma and whole blood spiked with Aspergillus conidia showed an identical lower detection limit (10 CFU), the sensitivity of plasma PCR was lower than that of PCR performed on whole blood samples.

Rapid detection of point mutations by fluorescence resonance energy transfer and probe melting curves in Candida species

BACKGROUND

The LightCycler(TM) combines rapid amplification of nucleic acids in glass capillaries with melting curve analysis based on fluorescence resonance energy transfer for the sensitive detection of point mutations in various settings, such as drug resistance and hereditary diseases. Point mutations leading to an altered structure of lanosteroldemethylase, the target enzyme of the fungistatic azoles, are an important mechanism of acquired resistance in Candida albicans.

METHODS

We screened 13 fluconazole-resistant C. albicans and 21 fluconazole-resistant C. tropicalis strains (minimum inhibitory concentration >128 mg/L), isolated from patients with AIDS, for the presence of defined point mutations by comparing conventional cycle sequencing with a newly designed LightCycler-based assay.

RESULTS

In C. tropicalis, 5 of 21 isolates showed the wild-type sequence, and 8 of 21 showed the homozygous nucleotide exchange thymine to cytosine at position 1554 (T1554C). A heterozygous genotype was detected in 8 of 21 isolates by the LightCycler, but in only 3 of 21 isolates by conventional cycle sequencing. In 2 of 13 C. albicans isolates, a homozygous point mutation leading to an amino acid exchange at position 464 (glycine to serine) was detected in both assays.

CONCLUSION

The LightCycler technique offers standardized, fast, sensitive, and reproducible detection of point mutations in different Candida spp.

Single dose radiosurgical treatment of recurrent previously irradiated primary brain tumors and brain metastases: final report of RTOG protocol 90-05

PURPOSE

To determine the maximum tolerated dose of single fraction radiosurgery in patients with recurrent previously irradiated primary brain tumors and brain metastases.

METHODS AND MATERIALS

Adults with cerebral or cerebellar solitary non-brainstem tumors </= 40 mm in maximum diameter were eligible. Initial radiosurgical doses were 18 Gy for tumors </= 20 mm, 15 Gy for those 21-30 mm, and 12 Gy for those 31-40 mm in maximum diameter. Dose was prescribed to the 50-90% isodose line. Doses were escalated in 3 Gy increments providing the incidence of irreversible grade 3 (severe) or any grade 4 (life threatening) or grade 5 (fatal) Radiation Therapy Oncology Group (RTOG) central nervous system (CNS) toxicity (unacceptable CNS toxicity) was < 20% within 3 months of radiosurgery. Chronic CNS toxicity was also assessed.

RESULTS

Between 1990-1994, 156 analyzable patients were entered, 36% of whom had recurrent primary brain tumors (median prior dose 60 Gy) and 64% recurrent brain metastases (median prior dose 30 Gy). The maximum tolerated doses were 24 Gy, 18 Gy, and 15 Gy for tumors </= 20 mm, 21-30 mm, and 31-40 mm in maximum diameter, respectively. However, for tumors < 20 mm, investigators' reluctance to escalate to 27 Gy, rather than excessive toxicity, determined the maximum tolerated dose. In a multivariate analysis, maximum tumor diameter was one variable associated with a significantly increased risk of grade 3, 4, or 5 neurotoxicity. Tumors 21-40 mm were 7.3 to 16 times more likely to develop grade 3-5 neurotoxicity compared to tumors < 20 mm. Other variables significantly associated with grade 3-5 neurotoxicity were tumor dose and Karnofsky Performance Status. The actuarial incidence of radionecrosis was 5%, 8%, 9%, and 11% at 6, 12, 18, and 24 months following radiosurgery, respectively. Forty-eight percent of patients developed tumor progression within the radiosurgical target volume. A multivariate analysis revealed two variables that were significantly associated with an increased risk of local progression, i.e. progression in the radiosurgical target volume. Patients with primary brain tumors (versus brain metastases) had a 2.85 greater risk of local progression. Those treated on a linear accelerator (versus the Gamma Knife) had a 2.84 greater risk of local progression. Of note, 61 % of Gamma Knife treated patients had recurrent primary brain tumors compared to 30% of patients treated with a linear accelerator.

CONCLUSIONS

The maximum tolerated doses of single fraction radiosurgery were defined for this population of patients as 24 Gy, 18 Gy, and 15 Gy for tumors </= 20 mm, 21-30 mm, and 31-40 mm in maximum diameter. Unacceptable CNS toxicity was more likely in patients with larger tumors, whereas local tumor control was most dependent on the type of recurrent tumor and the treatment unit.

Quantification of fungal DNA by using fluorescence resonance energy transfer and the light cycler system

The Light Cycler technique combines rapid in vitro amplification of DNA in glass capillaries with real-time species determination and quantification of DNA load. We have established a quantitative PCR protocol for two clinically important pathogens, Candida albicans and Aspergillus fumigatus. The sensitivity of the assay was comparable to those of previously described PCR protocols (5 CFU/ml). Specific detection of C. albicans and A. fumigatus could be achieved. The assay showed a high reproducibility of 96 to 99%. The assay was linear in a range between 10(1) and 10(4) Aspergillus conidia. As capillaries do not have to be reopened for post-PCR analysis, the risk of carryover contaminations could be minimized. The Light Cycler allowed quantification of the fungal loads in a limited number of clinical specimens from patients with hematological malignancies and histologically proven invasive fungal infections. Five of nine positive samples had fungal loads between 5 and 10 CFU/ml of blood, two of nine positive samples had fungal loads between 10 and 100 CFU/ml of blood, and two of nine samples had fungal loads of more than 100 CFU/ml of blood. All samples were also found to be PCR positive by PCR-enzyme-linked immunosorbent assay analysis.

Recurrent acute life-threatening events and lactic acidosis caused by chronic carbon monoxide poisoning in an infant

Acute severe carbon monoxide poisoning is usually easy to recognize and diagnose. However, chronic or less severe exposure may produce more subtle symptoms. We report on a 31/2-year-old girl who was admitted to the hospital several times with acute, life-threatening events, acidosis, and flu-like symptoms. The diagnosis was elusive, but after careful questioning of family members and a home visit, chronic carbon monoxide poisoning was diagnosed.

The G464S amino acid substitution in Candida albicans sterol 14alpha-demethylase causes fluconazole resistance in the clinic through reduced affinity

Fluconazole selectively inhibits fungal sterol 14alpha-demethylase, a cytochrome P450 enzyme found in plants, animals, fungi, and Mycobacteria. The mutation G464S, observed in the heme-binding domain of sterol 14alpha-demethylase in clinical strains of fluconazole-resistant Candida albicans, is shown here to cause resistance through substantially reducing the inhibitory effect of fluconazole and is associated with perturbation of the heme environment as indicated by spectral data. The protein exhibits 42% of the maximal enzymatic rate of the wild-type protein allowing continued production of the end product of fungal sterol biosynthesis, ergosterol, in resistant strains. This mutation may cause these phenotypes through altering the heme location, thus changing the ability of residues above the heme to bind the drug effectively. This perturbation would also account for the observation of reduced sterol demethylase catalytic activity by changing the location of the 14alpha-methyl group in relation to oxygen-bound heme during the catalytic cycle.