Validation of a DNA-Based Next-Generation Sequencing Test for Molecular Diagnostic Variant and Fusion Detection in Formalin-Fixed, Paraffin-Embedded Tissue Specimens and Liquid Biopsy Plasma/Cell-Free DNA Samples

This study evaluated two DNA-based next-generation sequencing approaches for detection of single-nucleotide variants (SNVs) and fusions in formalin-fixed, paraffin-embedded (FFPE) tissue specimens and liquid biopsies (AVENIO Targeted and Surveillance Panels). Reference standards (n = 7 with SNVs and structural variants) and real-world FFPE tissue specimens (n = 26 lung, colorectal, pancreas, ovary, breast, prostate, melanoma, and soft tissue cancer cases with n = 27 samples), liquid biopsies [n = 29 cases with n = 40 plasma/cell-free DNA (cfDNA) samples], and one pleural effusion (lung cancer) were analyzed by the AVENIO workflow for known SNVs (BRAF, BRCA1/2, CTNNB1, EGFR, KRAS, MET exon 14 skipping, NRAS, PIK3CA, and TP53), insertions and deletions (ERBB2 and KIT), and fusions (ALK and ROS1). Detection of SNVs, insertions and deletions, and fusions was reliable in 24 of 26 FFPE tissue specimen cases and at 1% allele frequency in 5 of 5 cfDNA reference standards and 37 of 40 plasma/cfDNA samples. Pitfalls were identified for the AVENIO workflow in calling and listing of clinically relevant variants, requiring additional manual inspection. Moreover, laboratory workflows are distinct for FFPE tissue specimens and liquid biopsies as well as time-consuming for sample quality control assays. In summary, the DNA-based next-generation sequencing approaches may be suitable for routine molecular pathology diagnostics on careful data interpretation and further optimization of the technical and laboratory workflows.

γδ T-cell Receptors Derived from Breast Cancer-Infiltrating T Lymphocytes Mediate Antitumor Reactivity

γδ T cells in human solid tumors remain poorly defined. Here, we describe molecular and functional analyses of T-cell receptors (TCR) from tumor-infiltrating γδ T lymphocytes (γδ TIL) that were in direct contact with tumor cells in breast cancer lesions from archival material. We observed that the majority of γδ TILs harbored a proinflammatory phenotype and only a minority associated with the expression of IL17. We characterized TCRγ or TCRδ chains of γδ TILs and observed a higher proportion of Vδ2⁺ T cells compared with other tumor types. By reconstructing matched Vδ2^- TCRγ and TCRδ pairs derived from single-cell sequencing, our data suggest that γδ TILs could be active against breast cancer and other tumor types. The reactivity pattern against tumor cells depended on both the TCRγ and TCRδ chains and was independent of additional costimulation through other innate immune receptors. We conclude that γδ TILs can mediate tumor reactivity through their individual γδ TCR pairs and that engineered T cells expressing TCRγ and δ chains derived from γδ TILs display potent antitumor reactivity against different cancer cell types and, thus, may be a valuable tool for engineering immune cells for adoptive cell therapies.

Nutritional status and metabolic risk in HIV-infected university students: challenges in their monitoring and management

Objective: This study aims to describe challenges in the management of HIV-infected university students focusing on their nutritional status and metabolic risk. Methods: A cross-sectional, descriptive study design was used to assess the anthropometry, food intake and clinical status of a cohort of known HIV-infected registered students at a South African university. Results: Participants n = 63) had a mean CD4 cell count of 411 (SD = 219.9) cells/mm3, a mean body mass index (BMI) of 28.05 (SD = 7.9) kg/m2 and only half of the participants (n = 31) were on antiretroviral therapy (ART). A higher BMI (> 25 kg/m2) was significantly (p < 0.05; V = 0.32) associated with higher CD4 cell counts of > 350 cells/mm3. Some 40% (n = 25) of students were at risk for metabolic complications based on their waist circumference and 11% (n = 7) had clinical signs of lipodystrophy. The ‘obese’ group consumed a mean energy intake of 24 kcal/kg bodyweight which was lower than the ‘overweight’ and normal weight groups. Conclusions: In total 51% of HIV-positive students in the sample presented with signs of metabolic complications. Side effects of ART can be prevented and/or treated by regular physical activity, adequate nutritional intake, monitoring of side effects and BMI, combined with optimal care and support. (Full text of the research articles are available online at www.medpharm.tandfonline.com/ojfp) S Afr Fam Pract 2017; DOI: 10.1080/20786190.2016.1248143

A novel thymoma-associated immunodeficiency with increased naive T cells and reduced CD247 expression

The mechanisms underlying thymoma-associated immunodeficiency are largely unknown, and the significance of increased blood γδ Τ cells often remains elusive. In this study we address these questions based on an index patient with thymoma, chronic visceral leishmaniasis, myasthenia gravis, and a marked increase of rare γδ T cell subsets in the peripheral blood. This patient showed cutaneous anergy, even though he had normal numbers of peripheral blood total lymphocytes as well as CD4(+) and CD8(+) T cells. Despite his chronic infection, analyses of immunophenotypes and spectratyping of his lymphocytes revealed an unusual accumulation of naive γδ and αβ T cells, suggesting a generalized T cell activation defect. Functional studies in vitro demonstrated substantially diminished IL-2 and IFN-γ production following TCR stimulation of his "untouched" naive CD4(+) T cells. Biochemical analysis revealed that his γδ and αβ T cells carried an altered TCR complex with reduced amounts of the ζ-chain (CD247). No mutations were found in the CD247 gene that encodes the homodimeric ζ protein. The diminished presence of CD247 and increased numbers of γδ T cells were also observed in thymocyte populations obtained from three other thymoma patients. Thus, our findings describe a novel type of a clinically relevant acquired T cell immunodeficiency in thymoma patients that is distinct from Good's syndrome. Its characteristics are an accumulation of CD247-deficient, hyporresponsive naive γδ and αβ T cells and an increased susceptibility to infections.

Surveillance of noise exposure in the Danish workplace: a baseline survey

AIMS

To evaluate an epidemiological approach to a national noise hazard surveillance strategy, and report current exposure levels in the Danish workplace.

METHODS

A study base of 840 companies in 10 selected high risk industries in the largest county in Denmark was identified from a national register. Noise exposure was measured among manual workers recruited from a random sample of workplaces in each industry. For reference, financial companies and a sample of residents were investigated according to the same protocol. The A-weighted equivalent sound level (L(Aeq)) for a full shift was measured by portable dosimeters worn by 830 workers employed at 91 workplaces (67% of 136 eligible companies).

RESULTS

The epidemiological design proved feasible and established a baseline for future noise surveillance. Substantial resources were needed to motivate workplaces to enlist and the final participation rate was less than optimal (66.9%). The L(Aeq (8)) values in the selected industries were highly elevated (mean 83.7 dB(A) (95% CI 83.3 to 84.1) in comparison with residents and office workers (mean 69.9 dB(A), 95% CI 68.8 to 71.0). Some 50% of the workers were exposed to more than 85 dB(A) and some 20% to more than 90 dB(A) in several industries.

CONCLUSION

Noise levels in Danish high risk industries remain high. A substantial proportion of workers are exposed to noise levels above the current threshold limit of 85 dB(A). Ongoing surveillance of noise exposure using full shift dosimetry of workers in random samples of workplaces most at risk to high noise levels may help reinforce preventive measures. Such a programme would benefit from compulsory workplace participation.

Stabilit�t der Osteosynthese bei Gelenkwalzenfrakturen in Klinik und biomechanischer Simulation

BACKGROUND

Fractures of the condylar head are traditionally managed by closed techniques, despite a considerable rate of dysfunctional problems. PDS pin osteosynthesis (presented by Rasse 1992) via a preauricular approach failed to become established as a standard procedure due to a lack of stability. Alternatively, mini- or microplating, as performed in our patients (101 condylar head fractures between 1993 and 2000), showed high-grade limitations of translatory movements in about 30% due to scarification after loosening of osteosynthesis materials. The aim of this study was to establish an efficient procedure for achieving a functionally stable and atraumatic osteosynthesis.

METHODS

For the definition of a suitable procedure, models of the mandible (standardized fractures, types A, B, and C) were osteosynthesized (six samples for each type of fracture and type of screw), each with three PDS pins, 2.0 mm resorbable, 2.0 cortical, 1.7 and 1.2 mm small fragment screws, and exposed to increasing loads in centric (0-20-35 mm opening) and eccentric (35 mm opening) condylar positions. A computerized biomechanical test stand allowed a dynamic simulation of chewing forces (16 hydraulic drives). The resulting fracture gaps were measured without contact by a motion capture system.

RESULTS

Within physiological limits, only 1.7 small fragment and 2.0 mm cortical screws were able to bear occlusal loadings up to 200 N (1.2 mm small fragment screws up to 150 N, resorbable 2.0 mm screws up to 100 N, and PDS-pins up to 50 N). In a pullout experiment (condylar spongious bone of young pigs, aged 4-6 months), 1.7 mm small fragment screws showed superior retention. A consecutively developed small fragment screw-system has been applied clinically in 74 condylar head fractures (58 patients). After removal of osteosynthesis material, 41 of 49 TM joints have so far shown complete restitution.

CONCLUSIONS

The newly developed osteosynthesis system using a retroauricular approach based on 1.7 mm small fragment screws makes maxillomandibular immobilization unnecessary. The extra-articular position of the screw heads prevents scar-induced articular limitations. Preexisting degenerative alterations of the TMJ soft tissues, however, will affect functional results adversely.

Evidence of clonality in chronic neutrophilic leukaemia

BACKGROUND

Chronic neutrophilic leukaemia (CNL) is a rare myeloproliferative disorder of elderly patients characterised by sustained neutrophilia and splenomegaly. The diagnosis of CNL requires the exclusion of BCR/ABL positive chronic myelogenous leukaemia (CML) and of leukaemoid reactions (LRs). The differentiation between CNL and LR is problematic because both conditions share similar morphological features; it is also important because patients with CNL generally have a poor prognosis.

AIMS

To determine whether CNL and LR could be distinguished on the basis of different clonality patterns.

METHODS

Blood samples from 52 women were studied using the human androgen receptor gene assay (HUMARA).

RESULTS

Monoclonality was found in the neutrophils in all 17 patients with different myeloproliferative syndromes (MPSs), including those with CNL. In four of the patients with CNL, autologous T cells were also monoclonal, suggesting that they belonged to the neoplastic clone. This finding was in contrast to other MPSs in which T cells were almost always polyclonal. Of nine patients with clinically suspected LR, the neutrophils of five were polyclonal, whereas three patients had monoclonal neutrophils, suggesting that they might be in the process of developing an MPS. Among 26 healthy blood donors, 20 had polyclonal neutrophils and five showed skewed clonality patterns. One case of LR and one normal blood donor were scored "not informative" at the HUMARA locus.

CONCLUSIONS

Clonality studies of blood neutrophils using HUMARA aid in distinguishing female patients with monoclonal CNL from those with LR. For the diagnosis of CNL, monoclonality of the neutrophils should be demonstrated whenever possible.

Missing HLA class I expression on Daudi cells unveils cytotoxic and proliferative responses of human gammadelta T lymphocytes

The major subset of human blood gammadelta T lymphocytes expresses the variable-region genes Vgamma9 and Vdelta2. These cells recognize non-peptidic phosphoantigens that are present in some microbial extracts, as well as the beta(2)-microglobulin-deficient Burkitt's lymphoma Daudi. Most cytotoxic human Vgamma9/Vdelta2 T cells express inhibitory natural killer cell receptors for HLA class I that downmodulate the responses of the gammadelta T lymphocytes against HLA class I expressing cells. In this study we show that transfection of the human beta(2)-microglobulin cDNA into Daudi cells markedly inhibits the cytotoxic and proliferative responses of human Vgamma9/Vdelta2 T cells. This provides direct evidence that the "innate" specificity of human Vgamma9/Vdelta2 T-lymphocytes for Daudi cells is uncovered by the loss of beta(2)m by Daudi. However, Daudi cells that express HLA class I in association with mouse beta(2)m at the cell surface are recognized by human Vgamma9/Vdelta2 T cells close to the same degree as the parental HLA class I deficient Daudi cell line. Thus, proper conformation of the HLA class I molecules is required for binding to natural killer cell receptors. Cloning of the HLA class I A, B, and C molecules of Daudi cells and transfer of the individual HLA class I molecules of Daudi cells into the HLA class I deficient recipient cell lines.221 and C1R demonstrate that for some human gammadelta T-cell clones cytolysis can be entirely inhibited by single HLA class I alleles while for other clones single HLA class I alleles only partially inhibit cytotoxicity. Thus, most human Vgamma9/Vdelta2 T cells represent a population of killer cells that evolved like NK cells to destroy target cells that have lost expression of individual HLA class I molecules but with a specificity that is determined by the Vgamma9/Vdelta2 TCR.

Investigations of intermediate host specificity help to elucidate the taxonomic status of Trichobilharzia ocellata (Digenea: Schistosomatidae)

The avian schistosomatid Trichobilharzia ocellata plays an important role as causative agent of cercarial dermatitis of humans in Europe. In order to improve the taxonomic knowledge on this parasite, studies of miracidial chemo-orientation as well as experimental infections of different snail species were conducted using strains of T. ocellata and T. franki. Both schistosomes exhibited a high intermediate host specificity. The miracidia clearly preferred the SCW (snail-conditioned water) of the respective natural intermediate host to SCW of other sympatric snail species. T. ocellata proved to be capable of infecting Lymnaea stagnalis and Stagnicola palustris, but could not develop in Radix ovata or R. auricularia. T. franki established an infection in specimens of R. auricularia and R. ovata, but not in L. stagnalis or S. palustris. The results imply that the intermediate host spectrum of T. ocellata is limited to L. stagnalis and S. palustris. Findings of T. ocellata (or Cercaria ocellata) that originated from snails of the genus Radix are likely to have actually belonged to species such as T. franki or T. regenti. The assumption that T. szidati is synonymous to T. ocellata is also discussed.

Observations on cercarial chaetotaxy as a means for the identification of European species of Trichobilharzia Skrjabin & Zakharow, 1920 (Digenea: Schistosomatidae)

In order to evaluate the importance of cercarial chaetotaxy in the identification of European avian schistosomatids of the genus Trichobilharzia Skrjabin & Zakharow, 1920, papillary patterns of T. franki Müller & Kimmig, 1994 and T. ocellata (La Valette, 1855) Brumpt, 1931 were examined and compared. Scanning electron microscopy (SEM) was also employed to confirm the number and distribution of the sensory papillae. The chaetotaxy of T. franki and T. ocellata were identical, which suggests a close kinship between the two species. Some sensory papillae stained insufficiently with silver nitrate or were difficult to examine using light microscopy. Thus, the use of SEM in future examinations of Trichobilharzia chaetotaxy will ensure the collection of data that are comparable between studies, even though some argentophilic structures are not visible using SEM.

[Incidence and predisposing factors of persistent backache after lumbar catheter epidural anesthesia in a non-obstetrical settingø]

OBJECTIVE

To determine the incidence of long term backache after lumbar epidural anesthesia with catheter (EPA) in the non-obstetrical setting.

DESIGN

Prospective 1-year follow-up study.

PATIENTS

All patients scheduled for elective arthroscopical surgery of the knee performed under EPA (n = 195).

INTERVENTIONS

A first questionnaire was sent to each patient three months after the operation. To chose patients reporting persistent backache after three months, a second questionnaire was sent one year after the operation.

MEASUREMENTS

Back pain before, within 5 days and at the time of the inquiry, i.e., three months and one year after EPA as well as patient satisfaction with the regional anesthetic. Statistic: contingency tables with Fisher's exact test (for categorical variables) and an unpaired t-Test (for continuous variables), p < 0.01 after adjustment for multiple testing (Bonferroni's method).

MAIN RESULTS

Response rate was 67%. Before EPA 23 patients (17.5%) complained of back pain. The short term incidence of back pain (i.e, within 5 days after EPA) was 24 out of 131 patients (18.3%) and not associated with pre-epidural back pain (p = 0.036, n.s.). 15 out of 131 patients (11.5%) reported persistent back pain after three months, 13 of them had complained of back pain before EPA (p < 0.0001). Thus, the incidence of new back pain 3 months after EPA was only 1.5%. 7 of the 15 patients returned the second questionnaire: 6 reported still persistent back pain, and all had complained of back pain before EPA. Age, height, weight, sex, duration of anesthesia and operation were not associated with long term back pain. Despite persistent back pain after three months 10 out of 15 patients would opt again for EPA.

CONCLUSION

The incidence of long term backache after EPA in the non-obstetrical setting is 11.5% and almost exclusively associated with pre-existing back pain. Biometrical factors seem to play no role. In patients with pre-existing back pain satisfaction with the anesthetic procedure might be improved by improving informed consent.

Veränderungen der Mikrozirkulation bei Patienten mit Unterschenkelerysipelen vor, während und nach antibiotischer Therapie

Bei 12 Patienten mit Erysipelen am Unterschenkel erfolgten Messungen der Mikrozirkulation in Ruhe und bei hämodynamischen Funktionstests. Bestimmt wurden: Hauttemperatur, Erythemstärke (a-Wert der Colorimetrie), transkutaner Sauerstoffpartialdruck (tcPO2 bei 37° C und 44° C Elektrodentemperatur) sowie Laser-Doppler-Flux (LDF). Die Messungen wurden im Zentrum der Erysipele und an den gesunden kontralateralen Beinen zu Beginn, während und eine Woche nach Ende der Antibiotikatherapie durchgeführt. Zum Zeitpunkt der akuten Entzündung zeigten alle Parameter deutliche Veränderungen; diese wiesen Reaktionsmuster auf, wie sie auch bei Dermatosen mit morphologischen Veränderungen des Kapillarsystems gefunden werden. Nach klinischer Abheilung wiesen tcPO2 bei 37° C und Laser-Doppler-Flux sowohl in Ruhe als auch bei den Funktionstests noch deutliche Veränderungen auf.

Control of B cell lymphoma recognition via natural killer inhibitory receptors implies a role for human Vgamma9/Vdelta2 T cells in tumor immunity

The Vgamma9/Vdelta2 T cell receptor (TCR) is expressed by most human gammadelta T cells. We show here that cytotoxic T lymphocytes of the Vgamma9/Vdelta2 subset, but not of the Vdelta1 subset of human gammadelta T cells, express natural killer inhibitory receptors (KIR) with specificity for different HLA class I alleles that down-regulate TCR-mediated signaling in response to HLA class I-expressing B cell lymphomas. Vgamma9/Vdelta2 T cell clones with a T helper cell phenotype lack KIR and produce lymphokines in response to most human B cell lymphomas, just as they do upon recognition of the HLA class I-deficient human Burkitt's lymphoma Daudi. Thus, human Vgamma9/Vdelta2 T cells have an innate specificity for nonpolymorphic cell surface structures expressed by many lymphoma cells and their cytotoxic activity is controlled by KIR. These results imply a general role of human Vgamma9/Vdelta2 T cells in the defense against hematopoietic tumors that is distinct from NK cells.