Module-detection approaches for the integration of multilevel omics data highlight the comprehensive response of Aspergillus fumigatus to caspofungin

Background

Omics data provide deep insights into overall biological processes of organisms. However, integration of data from different molecular levels such as transcriptomics and proteomics, still remains challenging. Analyzing lists of differentially abundant molecules from diverse molecular levels often results in a small overlap mainly due to different regulatory mechanisms, temporal scales, and/or inherent properties of measurement methods. Module-detecting algorithms identifying sets of closely related proteins from protein-protein interaction networks (PPINs) are promising approaches for a better data integration.

Results

Here, we made use of transcriptome, proteome and secretome data from the human pathogenic fungus Aspergillus fumigatus challenged with the antifungal drug caspofungin. Caspofungin targets the fungal cell wall which leads to a compensatory stress response. We analyzed the omics data using two different approaches: First, we applied a simple, classical approach by comparing lists of differentially expressed genes (DEGs), differentially synthesized proteins (DSyPs) and differentially secreted proteins (DSePs); second, we used a recently published module-detecting approach, ModuleDiscoverer, to identify regulatory modules from PPINs in conjunction with the experimental data. Our results demonstrate that regulatory modules show a notably higher overlap between the different molecular levels and time points than the classical approach. The additional structural information provided by regulatory modules allows for topological analyses. As a result, we detected a significant association of omics data with distinct biological processes such as regulation of kinase activity, transport mechanisms or amino acid metabolism. We also found a previously unreported increased production of the secondary metabolite fumagillin by A. fumigatus upon exposure to caspofungin. Furthermore, a topology-based analysis of potential key factors contributing to drug-caused side effects identified the highly conserved protein polyubiquitin as a central regulator. Interestingly, polyubiquitin UbiD neither belonged to the groups of DEGs, DSyPs nor DSePs but most likely strongly influenced their levels.

Conclusion

Module-detecting approaches support the effective integration of multilevel omics data and provide a deep insight into complex biological relationships connecting these levels. They facilitate the identification of potential key players in the organism’s stress response which cannot be detected by commonly used approaches comparing lists of differentially abundant molecules.

Electronic supplementary material

The online version of this article (10.1186/s12918-018-0620-8) contains supplementary material, which is available to authorized users.

Are we missing respiratory viral infections in infants and children? Comparison of a hospital-based quality management system with standard of care

OBJECTIVES

Hospital-based surveillance of influenza and acute respiratory infections relies on International Classification of Diseases (ICD) codes and hospital laboratory reports (Standard-of-Care). It is unclear how many cases are missed with either method, i.e. remain undiagnosed/coded as influenza and other respiratory virus infections. Various influenza-like illness (ILI) definitions co-exist with little guidance on how to use them. We compared the diagnostic accuracy of standard surveillance methods with a prospective quality management (QM) programme at a Berlin children's hospital with the Robert Koch Institute.

METHODS

Independent from routine care, all patients fulfilling pre-defined ILI-criteria (QM-ILI) participated in the QM programme. A separate QM team conducted standardized clinical assessments and collected nasopharyngeal specimens for blinded real-time quantitative PCR for influenza A/B viruses, respiratory syncytial virus, adenovirus, rhinovirus and human metapneumovirus.

RESULTS

Among 6073 individuals with ILI qualifying for the QM programme, only 8.7% (528/6073) would have undergone virus diagnostics during Standard-of-Care. Surveillance based on ICD codes would have missed 61% (359/587) of influenza diagnoses. Of baseline ICD codes, 53.2% (2811/5282) were non-specific, most commonly J06 ('acute upper respiratory infection'). Comparison of stakeholder case definitions revealed that QM-ILI and the WHO ILI case definition showed the highest overall sensitivities (84%-97% and 45%-68%, respectively) and the CDC ILI definition had the highest sensitivity for influenza infections (36%, 95% CI 31.4-40.8 for influenza A and 48%, 95% CI 40.5-54.7 for influenza B).

CONCLUSIONS

Disease-burden estimates and surveillance should account for the underreporting of cases in routine care. Future studies should explore the effect of ILI screening and surveillance in various age groups and settings. Diagnostic algorithms should be based on the WHO ILI case definition combined with targeted testing.

Building a New Model of Care for Rapid Breast Radiotherapy Treatment Planning: Evaluation of the Advanced Practice Radiation Therapist in Cavity Delineation

AIMS

Breast radiotherapy treatment is commonly managed by a multidisciplinary team to ensure optimal delivery of care. We sought a new model of care whereby a clinical specialist radiation therapist (CSRT) delineates the cavity target for whole breast radiotherapy treatment planning and the radiation oncologist validates the contour during final plan review. This study evaluated the radiation oncologist's acceptance of these contours and identified characteristics of cavities suitable for CSRT-directed contouring.

MATERIALS AND METHODS

Following specialised breast oncology education and training by the radiation oncologist, the CSRT prospectively delineated cavities in 30 tangential breast radiotherapy cases and consulted the radiation oncologist in 'complex' cases but directed 'non-complex' cases for treatment planning. Changes to CSRT contours were evaluated using the conformity index. Breast density, time since surgery and cavity location, size and visualisation score [CVS: range 1 (no visible cavity) to 5 (homogenous cavity)] were captured.

RESULTS

Of the 30 CSRT delineated cavities contours, the CSRT directed 20 (66.7%) cases for planning without radiation oncology review; 19 were accepted (without changes) by the radiation oncologist upon final plan review and one was changed by the radiation oncologist (conformity index = 0.93) for boost treatment and did not affect the tangential treatment plan. Ten (33.3%) cases, all CVS ≤ 3, were reviewed with the radiation oncologist before planning (conformity index = 0.88 ± 0.12). CVS was inversely correlated with breast density and cavity size (P < 0.01).

CONCLUSIONS

The CSRT delineated cavities appropriate for clinical radiotherapy treatment planning in women with well-visualised cavities, whereas 'complex' cases with dense breast parenchyma, CVS ≤ 3, and/or cases needing boost radiotherapy treatment required review with the radiation oncologist before planning.

[Locking attachment plate - first experience]

BACKGROUND

In this paper we present our first experience in the application of a new, fixed-angle plate fixation: the locking attachment plate (LAP, Synthes, Oberdorf, Switzerland). We examined whether the LAP is a useful addition to the existing technical palette for periprosthetic fractures. The LAP is used for periprosthetic fractures with stable prostheses or intramedullary implants. The plate can be installed, e.g., on a 4.5 mm locking compression plate (LCP). Locking screws or cortical screws can be placed through its 4 diagonal fixed-angle arms, bicortical around the prosthesis stem into the bone. The LAP is designed to prevent lateral screw pull-out, to stabilise the prosthesis stem and thus to allow early postoperative mobilisation of patients.

PATIENTS AND METHODS

We implanted the LAP by operative fracture-treatment in the ORIF technique in 17 patients with periprosthetic fractures of the femur, tibia and humerus. The follow-up was at least 13 months.

RESULTS

There were two losses to follow-up: the patients died a few weeks postoperatively. There was a total of two of 17 cases with infection events (11.8 %). We could examine 15 patients for follow-up. Eleven of these 15 patients regained their original range of motion (ROM) and nine of 15 patients their pretraumatic mobility. In all cases with periprosthetic humeral fractures we detected muscular deficits. In five out of 15 cases (33.3 %) no radiological fracture healing could be observed. Nevertheless in 14 of 15 cases the implant was stable without signs of implant or prosthetic loosening. There was no case of material failure.

CONCLUSION

Periprosthetic fractures are an increasingly common complication in old, often multi-morbid patients. A contemporary therapeutic intervention and early postoperative mobilisation contribute substantially to the success of treatment. The first results in the use of the LAP as a new implant option for periprosthetic fractures of the femur, tibia and humerus are promising. Further studies are necessary to show whether our overall good results are reproducible in larger groups of patients and whether the LAP can be given a firm position in the technical repertoire for treatment of periprosthetic fractures.

Sites of gastric cancer recurrence after adjuvant chemoradiotherapy

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Background: Since the Intergroup 0116 study in 2000, adjuvant post-operative chemoradiotherapy (CRT) has been offered routinely to similar patients with resected gastric cancer at Princess Margaret Hospital (PMH) using CT-planned and 3D conformal/intensity modulated radiotherapy (RT). The objective of this study was to analyze patterns of recurrence with respect to RT treatment volumes.

Methods: Date and site (local, locoregional or distant) of first recurrence data was obtained from chart review for all patients treated at PMH with adjuvant CRT for resected gastric adenocarcinoma (Jan. 1, 2000-Nov. 30, 2009). Patients whose recurrences were limited to local (gastric remnant, duodenal margin, gastric bed recurrence) and/or regional sites (regional lymph node recurrence) were selected for analysis. When available, diagnostic imaging of recurrence site was registered to the original planning RT dataset. The center of mass for each recurrence was identified as a point and its location categorized according to the isodose encompassing it; in-field (≥ 90%), marginal (50%-89%), and out-of-field (< 50%).

Results: Three-year OS, and RFS were 66% (95% CI: 58-73) and 58% (50-60), respectively. Of 203 patients treated, 75 recurrences were identified (Table). Of the 13 local/locoregional recurrences, 4 were in-field, 1 marginal, 1 could not be registered due to change in body habitus, and 7 did not have an available original dataset.

Conclusions: Rates of isolated local and/or regional recurrence in this study were low. This represents a change in the pattern seen with surgery alone suggesting the addition of CRT results in decreased isolated local and/or regional recurrence. Of the small number of local and/or regional recurrences available for analysis, all were in-field or marginal. Further studies involving a larger cohort of patients might allow for more meaningful analysis of trends in recurrence site with evolving RT techniques.

[Table: see text]

No significant financial relationships to disclose.

A clinical trial of creatine in ALS

BACKGROUND

Mitochondrial dysfunction occurs early in the course of ALS, and the mitochondria may be an important site for therapeutic intervention. Creatine stabilizes the mitochondrial transition pore, and is important in mitochondrial ATP production. In a transgenic mouse model of ALS, administration of creatine prolongs survival and preserves motor function and motor neurons.

METHODS

The authors conducted a randomized double-blind, placebo controlled trial on 104 patients with ALS from 14 sites to evaluate the efficacy of creatine supplementation in ALS. The primary outcome measure was maximum voluntary isometric contraction of eight upper extremity muscles, with secondary outcomes including grip strength, ALS Functional Rating Scale-Revised, and motor unit number estimates. Patients were treated for 6 months, and evaluated monthly.

RESULTS

Creatine was tolerated well, but no benefit of creatine could be demonstrated in any outcome measure. CI analysis showed that the study, although powered to detect a 50% or greater change in rate of decline of muscle strength, actually made an effect size of greater than 23% unlikely. It was also demonstrated that motor unit number estimation was performed with acceptable reproducibility and tolerability, and may be a useful outcome measure in future clinical trials.

CONCLUSION

Any beneficial effect of creatine at 5 g per day in ALS must be small. Other agents should be considered in future studies of therapeutic agents to address mitochondrial dysfunction in ALS. In addition, motor unit number estimation may be a useful outcome measure for future clinical trials in ALS.

A comparison of different challenge methods for induction of atrophic rhinitis in pigs

Transmission and development of atrophic rhinitis (AR) was studied in 5- to 15-week-old pigs (Groups 2-7) originating from a herd free of AR, and compared to unexposed healthy pigs (Group 1), and pigs from a herd with endemic AR (Group 8). At the start of the trial, pigs in Groups 2-5 were challenged intranasally twice a week for 3 weeks with pure cultures of bacteria originating from the endemic AR herd: Nontoxigenic Pasteurella multocida type A (PmA) plus Bordetella bronchiseptica phase I (Bb) (Group 2); PmA + toxigenic Pm type D (PmD) (Group 3); PmD only (Group 4); and PmD + Bb (Group 5). Group 6 pigs were challenged with nasal wash of pigs from the endemic AR herd, and Group 7 pigs were challenged by being housed together in the same pen with Group 8 pigs throughout the study. Nasal swabs of all pigs were cultured 5 times during the study. Serum was collected at 6 weeks post challenge. Average daily gain (ADG) and turbinate lesions (turbinate gross lesions by visual scoring and by Turbinate Perimeter Ratio, TPR, scoring, and histopathological lesions) were measured at the time of slaughter at 15 weeks of age. Mean TPR value for the Group 1 pigs was 1.64, which was significantly (P less than 0.05) different from the mean TPR value of 0.58 for the pigs from the endemic AR herd (Group 8), the 0.79 value for Group 6 pigs, and 1.03 value for Group 7 pigs. Of pigs challenged with pure bacterial cultures, only Group 5 (PmD + Bb) developed significant AR (mean TPR = 1.24). Only one pig in each of Groups 2 and 3, and two pigs in Group 4 showed TPR values indicative of AR (TPR less than 1.30). However, histopathological examination showed that those pigs were recovering from the infection 7 weeks post challenge. Constant exposure to certain bacteria or other factors in nasal washings, stress of crowding or poor environmental conditions might be required to experimentally produce AR in 5-week and older pigs similar to that in naturally infected pigs. There was no relationship between turbinate lesions and the isolation frequency or quantity of PmA, PmD, or Bb. Antibody levels against PmA or PmD had moderate to high correlation with TPR values (r = -0.694 and -0.503 respectively). ELISA values also corresponded well with the type of bacteria inoculated in each group of pigs and appeared to be a sensitive test for PmA, PmD, and Bb infections in pigs.(ABSTRACT TRUNCATED AT 400 WORDS)

A quantitative study of dendrite complexity in selected areas of the human cerebral cortex

This study seeks relationships between the degree of dendrite complexity of four areas of the human cerebral cortex and the type of function subserved by those areas. Quantitative studies of basilar dendrite patterns in the trunk and hand-finger receptive zones of areas 3 and 1, superior gyrus of the prefrontal cortex (area 9), and supramarginal gyrus (area 39) of the parietal lobe, in the left hemisphere of 10 subjects are reported. Measurements of dendrite complexity were based on the Sholl method of counting dendrite intersections with a series of superimposed concentric rings centered on the middle of the neuron soma. The data were analyzed graphically to show (1) characteristic dendrite profiles generated by cells in each of these areas, (2) comparisons between dendrite systems of two paired areas, i.e., trunk vs. hand-finger, and hand-finger vs. supramarginal, and (3) cumulative dendrite-ring intersection patterns for all areas studied. The data provided only partial support for our working hypothesis suggesting a relationship between complexity of the dendrite arbor and the nature of the computational tasks performed by the area. However, complexity of dendrite systems in the trunk area was found to be generally less than that of any other. In addition, there were suggestive associations between the complexity of dendrite systems of the hand-finger zone of the primary sensory receptive area and the nature of the work with which the individual had been associated during his/her working life. It proved more difficult to discern relationships between structure and function in the cortical associative areas. The study underlines the large degree of interindividual variation in dendrite structure and the need for much more extensive information about the life history of individuals who serve as subjects for this type of study.

Malignant human B cells express two populations of p24 surface antigens

Monoclonal antibodies (MoAb) to a leukemia-associated p24 cell surface antigen are currently being used to purge bone marrow of malignant cells before autologous transplantation for acute lymphoblastic leukemia (ALL). Their use as potential diagnostic reagents for hematologic disorders is also under investigation. It has been assumed throughout these investigations that the p24-specific MoAb produced by different laboratories all identify the same antigen. Our present studies indicate that at least two populations of p24 antigens, having different chemical properties and cellular distributions, exist on malignant B cells. For example, eight MoAb raised to ALL cells (ALL-MoAb) identify a p24 antigen on these cells but do not react with the Burkitt's lymphoma cell line Ramos. In contrast, six MoAb raised to Ramos (Ramos-MoAb) identify a p24 antigen on both Ramos and ALL cells. Quantitative binding of both sets of MoAb to ALL cells is comparable. The ALL-MoAb react with platelets, granulocytes, and activated but not resting T lymphocytes, whereas the Ramos-MoAb react with both resting and activated T lymphocytes but not with platelets or granulocytes. The ALL-MoAb react with 11 of 34 human hematopoietic cell lines tested; the Ramos-MoAb react with all 34. Both sets of MoAb react with most of the nonhematopoietic human cell lines tested. Reciprocal exhaustive radioimmune precipitation experiments performed with an ALL cell line indicate that the antigenic determinants recognized by these two sets of MoAb are present on different molecules. Similarly, proteolytic digests of iodinated antigens identified by these two sets of MoAb on ALL cells confirm the unique chemical identities of these molecules and suggest that they reflect the products of different genetic loci. The presence of the antigen identified by the Ramos-MoAb on every cell population tested except granulocytes suggests that it may serve an important cellular function. The existence of two populations of p24 antigens on at least some hematopoietic cells indicates the need for caution when comparing the results of studies of these antigens by groups employing different MoAb.

Malignant human B cells express two populations of p24 surface antigens

Monoclonal antibodies (MoAb) to a leukemia-associated p24 cell surface antigen are currently being used to purge bone marrow of malignant cells before autologous transplantation for acute lymphoblastic leukemia (ALL). Their use as potential diagnostic reagents for hematologic disorders is also under investigation. It has been assumed throughout these investigations that the p24-specific MoAb produced by different laboratories all identify the same antigen. Our present studies indicate that at least two populations of p24 antigens, having different chemical properties and cellular distributions, exist on malignant B cells. For example, eight MoAb raised to ALL cells (ALL-MoAb) identify a p24 antigen on these cells but do not react with the Burkitt's lymphoma cell line Ramos. In contrast, six MoAb raised to Ramos (Ramos-MoAb) identify a p24 antigen on both Ramos and ALL cells. Quantitative binding of both sets of MoAb to ALL cells is comparable. The ALL-MoAb react with platelets, granulocytes, and activated but not resting T lymphocytes, whereas the Ramos-MoAb react with both resting and activated T lymphocytes but not with platelets or granulocytes. The ALL-MoAb react with 11 of 34 human hematopoietic cell lines tested; the Ramos-MoAb react with all 34. Both sets of MoAb react with most of the nonhematopoietic human cell lines tested. Reciprocal exhaustive radioimmune precipitation experiments performed with an ALL cell line indicate that the antigenic determinants recognized by these two sets of MoAb are present on different molecules. Similarly, proteolytic digests of iodinated antigens identified by these two sets of MoAb on ALL cells confirm the unique chemical identities of these molecules and suggest that they reflect the products of different genetic loci. The presence of the antigen identified by the Ramos-MoAb on every cell population tested except granulocytes suggests that it may serve an important cellular function. The existence of two populations of p24 antigens on at least some hematopoietic cells indicates the need for caution when comparing the results of studies of these antigens by groups employing different MoAb.

Anti-CALLA antibodies identify unique antigens on lymphoid cells and granulocytes

The common acute lymphoblastic leukemia antigen (CALLA) is a 100-kd surface glycoprotein that is present on normal and malignant lymphoid cells. It is a useful marker for distinguishing between clinically important types of acute leukemia. Anti-CALLA monoclonal antibodies (MoAb) also react with mature myeloid cells (granulocytes), where they identify an antigen having a similar molecular weight (mol wt). We now report that the antigens detected by anti-CALLA MoAb on human lymphoid and myeloid cells differ in their behavior and chemistry. Surface-labeling studies indicate that the antigen on lymphoid cells has a mol wt of approximately 100 kd v 110 kd for that on granulocytes. When cells are metabolically labeled with 35S-methionine, differences in the mol wt of these antigens are again observed. Unlike the lymphoid antigen, expression of that on purified granulocytes is not modulated by incubation with specific antibody. Sodium dodecyl sulfate-polyacrylamide gel electrophoresis analysis of proteolytic digests of the two antigens fails to clarify their chemical relationship. Thus the antigens detected on these two cell types may share an epitope(s) but be chemically distinct, or CALLA may exist in distinct forms and behave differently on lymphoid cells and granulocytes.