Construction and benchmarking of a multi-ethnic reference panel for the imputation of HLA class I and II alleles

Genotype imputation of the human leukocyte antigen (HLA) region is a cost-effective means to infer classical HLA alleles from inexpensive and dense SNP array data. In the research setting, imputation helps avoid costs for wet lab-based HLA typing and thus renders association analyses of the HLA in large cohorts feasible. Yet, most HLA imputation reference panels target Caucasian ethnicities and multi-ethnic panels are scarce. We compiled a high-quality multi-ethnic reference panel based on genotypes measured with Illumina’s Immunochip genotyping array and HLA types established using a high-resolution next generation sequencing approach. Our reference panel includes more than 1,300 samples from Germany, Malta, China, India, Iran, Japan and Korea and samples of African American ancestry for all classical HLA class I and II alleles including HLA-DRB3/4/5. Applying extensive cross-validation, we benchmarked the imputation using the HLA imputation tool HIBAG, our multi-ethnic reference and an independent, previously published data set compiled of subpopulations of the 1000 Genomes project. We achieved average imputation accuracies higher than 0.924 for the commonly studied HLA-A, -B, -C, -DQB1 and -DRB1 genes across all ethnicities. We investigated allele-specific imputation challenges in regard to geographic origin of the samples using sensitivity and specificity measurements as well as allele frequencies and identified HLA alleles that are challenging to impute for each of the populations separately. In conclusion, our new multi-ethnic reference data set allows for high resolution HLA imputation of genotypes at all classical HLA class I and II genes including the HLA-DRB3/4/5 loci based on diverse ancestry populations.

Vedolizumab is associated with changes in innate rather than adaptive immunity in patients with inflammatory bowel disease

OBJECTIVE

Vedolizumab, a monoclonal antibody directed against the integrin heterodimer α4β7, is approved for the treatment of Crohn's disease and ulcerative colitis. The efficacy of vedolizumab has been suggested to result from inhibition of intestinal T cell trafficking although human data to support this conclusion are scarce. We therefore performed a comprehensive analysis of vedolizumab-induced alterations in mucosal and systemic immunity in patients with inflammatory bowel disease (IBD), using anti-inflammatory therapy with the TNFα antibody infliximab as control.

DESIGN

Immunophenotyping, immunohistochemistry, T cell receptor profiling and RNA sequencing were performed using blood and colonic biopsies from patients with IBD before and during treatment with vedolizumab (n=18) or, as control, the anti-TNFα antibody infliximab (n=20). Leucocyte trafficking in vivo was assessed using single photon emission computed tomography and endomicroscopy.

RESULTS

Vedolizumab was not associated with alterations in the abundance or phenotype of lamina propria T cells and did not affect the mucosal T cell repertoire or leucocyte trafficking in vivo. Surprisingly, however, α4β7 antibody treatment was associated with substantial effects on innate immunity including changes in macrophage populations and pronounced alterations in the expression of molecules involved in microbial sensing, chemoattraction and regulation of the innate effector response. These effects were specific to vedolizumab, not observed in response to the TNFα antibody infliximab, and associated with inhibition of intestinal inflammation.

CONCLUSION

Our findings suggest that modulation of innate immunity contributes to the therapeutic efficacy of vedolizumab in IBD.

TRIAL REGISTRATION NUMBER

NCT02694588.

RNA based individualized drug selection in breast cancer patients without patient-matched normal tissue

Background

While standard RNA expression tests stratify patients into risk groups, RNA-Seq can guide personalized drug selection based on expressed mutations, fusion genes, and differential expression (DE) between tumor and normal tissue. However, patient-matched normal tissue may be unavailable. Additionally, biological variability in normal tissue and technological biases may confound results. Therefore, we present normal expression reference data for two sequencing methods that are suitable for breast biopsies.

Results

We identified breast cancer related and drug related genes that are expressed uniformly across our normal samples. Large subsets of these genes are identical for formalin fixed paraffin embedded samples and fresh frozen samples. Adipocyte signatures were detected in frozen compared to formalin samples, prepared by surgeons and pathologists, respectively. Gene expression confounded by adipocytes was identified using fat tissue samples. Finally, immune repertoire statistics were obtained for healthy breast, tumor and fat tissues.

Conclusions

Our reference data can be used with patient tumor samples that are asservated and sequenced with a matching aforementioned method. Coefficients of variation are given for normal gene expression. Thus, potential drug selection can be based on confidently overexpressed genes and immune repertoire statistics.

Materials and Methods

Normal expression from formalin and frozen healthy breast tissue samples using Roche Kapa RiboErase (total RNA) (19 formalin, 9 frozen) and Illumina TruSeq RNA Access (targeted RNA-Seq, aka TruSeq RNA Exome) (11 formalin, 1 frozen), and fat tissue (6 frozen Access). Tumor DE using 10 formalin total RNA tumor samples and 1 frozen targeted RNA tumor sample.

The Changing Landscape of Naive T Cell Receptor Repertoire With Human Aging

Human aging is associated with a profound loss of thymus productivity, yet naïve T lymphocytes still maintain their numbers by division in the periphery for many years. The extent of such proliferation may depend on the cytokine environment, including IL-7 and T-cell receptor (TCR) “tonic” signaling mediated by self pMHCs recognition. Additionally, intrinsic properties of distinct subpopulations of naïve T cells could influence the overall dynamics of aging-related changes within the naïve T cell compartment. Here, we investigated the differences in the architecture of TCR beta repertoires for naïve CD4, naïve CD8, naïve CD4⁺CD25⁻CD31⁺ (enriched with recent thymic emigrants, RTE), and mature naïve CD4⁺CD25⁻CD31⁻ peripheral blood subsets between young and middle-age/old healthy individuals. In addition to observing the accumulation of clonal expansions (as was shown previously), we reveal several notable changes in the characteristics of T cell repertoire. We observed significant decrease of CDR3 length, NDN insert, and number of non-template added N nucleotides within TCR beta CDR3 with aging, together with a prominent change of physicochemical properties of the central part of CDR3 loop. These changes were similar across CD4, CD8, RTE-enriched, and mature CD4 subsets of naïve T cells, with minimal or no difference observed between the latter two subsets for individuals of the same age group. We also observed an increase in “publicity” (fraction of shared clonotypes) of CD4, but not CD8 naïve T cell repertoires. We propose several explanations for these phenomena built upon previous studies of naïve T-cell homeostasis, and call for further studies of the mechanisms causing the observed changes and of consequences of these changes in respect of the possible holes formed in the landscape of naïve T cell TCR repertoire.

Overview of methodologies for T-cell receptor repertoire analysis

Background

The T-cell receptor (TCR), located on the surface of T cells, is responsible for the recognition of the antigen-major histocompatibility complex, leading to the initiation of an inflammatory response. Analysing the TCR repertoire may help to gain a better understanding of the immune system features and of the aetiology and progression of diseases, in particular those with unknown antigenic triggers. The extreme diversity of the TCR repertoire represents a major analytical challenge; this has led to the development of specialized methods which aim to characterize the TCR repertoire in-depth. Currently, next generation sequencing based technologies are most widely employed for the high-throughput analysis of the immune cell repertoire.

Results

Here, we report on the latest methodological advancements in the field by describing and comparing the available tools; from the choice of the starting material and library preparation method, to the sequencing technologies and data analysis.

Finally, we provide a practical example and our own experience by reporting some exemplary results from a small internal benchmark study, where current approaches from the literature and the market are employed and compared.

Conclusions

Several valid methods for clonotype identification and TCR repertoire analysis exist, however, a gold standard method for the field has not yet been identified. Depending on the purpose of the scientific study, some approaches may be more suitable than others. Finally, due to possible method specific biases, scientists must be careful when comparing results obtained using different methods.

Electronic supplementary material

The online version of this article (doi:10.1186/s12896-017-0379-9) contains supplementary material, which is available to authorized users.

Enhancement of Lysosomal Glycohydrolase Activity in Human Primary B Lymphocytes during Spontaneous Apoptosis

It has been shown that lysosomes are involved in B cell apoptosis but lysosomal glycohydrolases have never been investigated during this event. In this study we determined the enzymatic activities of some lysosomal glycohydrolases in human tonsil B lymphocytes (TBL) undergoing in vitro spontaneous apoptosis. Fluorimetric methods were used to evaluate the activities of β-hexosaminidases, α-mannosidase, β-mannosidase, β-galactosidase, β-glucuronidase and α-fucosidase. Results show that in TBL during spontaneous apoptosis, there is a significant increase in the activity of β-hexosaminidases, α-mannosidase, β-mannosidase and β-galactosidase. Also β-glucuronidase and α-fucosidase activities increase but not in a significant manner. Further studies on β-hexosaminidases revealed that also mRNA expression of the α- and β-subunits, which constitute these enzymes, increases during spontaneous TBL apoptosis. When TBL are protected from apoptosis by the thiol molecule N-acetyl-L-cysteine (NAC), there is no longer any increase in glycohydrolase activities and mRNA expression of β-hexosaminidase α- and β-subunits. This study demonstrates for the first time that the activities and expression of some lysosomal glycohydrolases are enhanced in TBL during spontaneous apoptosis and that these increases are prevented when TBL apoptosis is inhibited.

Effects of perceptive rehabilitation on balance control in patients with Parkinson's disease

BACKGROUND

Subjects affected by Parkinson's disease have substantially impaired static and dynamic balance, leading to diminished functional ability. Conventional and innovative exercises have been suggested, but most of them were focused on motor features of posture and gait, deserving poor attention to perceptive aspects of balance.

OBJECTIVE

To evaluate the efficacy of the perceptive rehabilitation, based on perceptual surfaces, for postural balance (primary aim) and pain, depression and activity daily living.

METHODS

In this pilot study, we have treated 9 patients with Parkinson's disease undergone rehabilitation aiming to restoring their correct body midline perception, according a schema treatment - no treatment - treatment.

RESULTS

During the rehabilitative intervention, both Tinetti balance score (p = 0.007 in both phases) and Tinetti gait score (p = 0.011 and p = 0.016, respectively), such as pain relief assessed by Visual Analogue Scale (p = 0.011, p = 0.010) were improved. Conversely in the phase of no-intervention, lasting the same amount of time, it was showed a significant reduction of Tinetti Balance score (p = 0.010) and no significant changes in terms of Tinetti Gait score and Visual Analogue Scale.

CONCLUSIONS

These preliminary results highlighted the importance of introducing perceptive training into the exercises proposed to patients with Parkinson's disease for reducing both their static and dynamic balance impairments.

Emergency transanal haemorrhoidal Doppler guided dearterialization for acute and persistent haemorrhoidal bleeding

AIM

The effectiveness of Doppler guided transanal haemorrhoidal dearterialization (THD) for arresting persistent haemorrhoidal bleeding in patients admitted as an emergency was studied.

METHOD

Eleven patients with severe anal bleeding underwent emergency THD as definitive treatment for haemorrhoids. In the majority of patients antiplatelet or anticoagulant therapy was ongoing and severe anaemia was present in six patients.

RESULTS

The mean operative time was 39.7 min. Six to nine feeding arteries were ligated. Intra-operative blood loss was nil. Bleeding was well controlled in all patients. No blood transfusion was required. Mean pain score per verbal numeric scale was 3.6 and 1.4 on day 1 and day 3 respectively. The mean time to resumption of normal activities was 8 days. No major complications were experienced. Six months follow-up demonstrated good control of haemorrhoidal disease.

CONCLUSION

THD is effective in controlling acute haemorrhoidal bleeding with a low incidence of postoperative complications.

Silica particle size and shape: in vitro effects on extracellular matrix metabolism and viability of human bronchial epithelial cells

Crystal micro-morphology and dimension of silica particles could be responsible for the high prevalence of silicosis as recently found among goldsmiths. In the present study we investigated two samples of silica particles with different surface sizes and shapes for their capacity to induce changes in ECM component production. In addition we investigated if their different effects could be related to cytotoxicity and apoptotic effects. Human bronchial epithelial cells were cultured with or without a sample of Silica used for casting gold jewellery, named in our experiments Silica P or a commercial sample of Silica with different physical and chemical properties, named in our experiments Silica F. After 48 h of exposure PCR analysis determined levels of several matrix components. As induction of the apoptosis cascade, annexin assay, caspase 3 activity and cellular cytoxicity by MTT assay were assayed. Silica F promoted fibronectin, MMP12, tenascin C and Integrins b5 gene expressions more than Silica P. Silica P stimulated more TGFß1 and its TGFßR1 receptor than Silica F. Cytotoxic effects were induced by the two samples of Silica. On the contrary, no alteration in classic apoptotic marker protein expression was observed in presence of either Silica F or Silica P, suggesting silica particles affect ECM production and metalloproteases through a mechanism that does not involve apoptotic activation. Different Silica micromorphology and TGFß signal pathway are linked to lung fibrotic effects but the potential role Silica in apoptotic and toxic reaction remains to be ascertained.

[Assessment and monitoring of organizational appropriateness of inpatient rehabilitation facilities in Lazio region: tools and working methods, results and comparison with other regional experiences]

Aim of this paper is to analyze the tools and working methods, used in the Lazio Region, to assess organizational appropriateness in the context of Inpatient Rehabilitation Facilities, and the results obtained. It illustrates also the regional experiences of Veneto and Lombardia, which characterized by dynamism and originality in an attempt to overcome the obvious place for the critical assessment of this area of care.

[Multicentric study to evaluate the quality of discharge abstract coding of admissions in which the treatment was not performed and to identify a possible appropriateness indicator]

The aim of this study was to assess the quality of discharge abstract data regarding admissions in which the planned treatment was not performed, in 4 hospitals in the Rome metropolitan area. The main objective was to evaluate the appropriateness of admissions through use of the Italian version of the Appropriateness Evaluation Protocol (AEP/PRUO). Inconsistencies between discharge abstract forms and hospital records were found in 95/142 (66,9%) of examined records. These were subsequently evaluated through the Appropriateness Evaluation Protocol and overall , 95,6% of inconsistent records were found to be inappropriate admissions. Monitoring V64 codes may represent an indirect indicator of appropriateness.

Minimal handling and bronchopulmonary dysplasia in extremely low-birth-weight infants

Over the last 16 years a minitouch regime, i.e., nasal continuous positive airway pressure (n-CPAP) and/or nasal intermittent positive pressure ventilation (n-IPPV), together with a minimal intubation policy has been routinely used for the treatment of respiratory distress syndrome (RDS) in preterm infants. Only 1.39 (1 out of 72) of the extremely low-birth-weight babies admitted to our Neonatal Intensive Care Unit (NICU) and surviving for at least 36 weeks' postconceptional age developed bronchopulmonary dysplasia at 36 weeks (BPD 36-wk). The BPD-36 wk incidence observed in our population is significantly lower than expected (30%) from the literature (p=0.000002).

CONCLUSION

Our experience supports the effectiveness of the minitouch regime as a way to ventilate premature babies, reducing BPD risk.

[Statine and endothelium dysfunction in diabetes]

Diabetes is associated with significant morbidity and mortality in the setting of acute coronary syndromes. Exists a progressive relationship between glucose levels and cardiovascular risk. Hyperglycemy in fact produces endothelial dysfunction recognised to be a key accessory to diabetic microangiopathy and macroangiopathy. Furthermore diabetics present high levels of cholesterol which elevate the risk of CHD. The statins, for their effects, may represent the fit therapy. The beneficial effects of statins may extend beyond improving the lipid profile. There are several proposed mechanisms for event reduction by lipid-lowering therapy, which include improved endothelium-dependent vasodilation, stabilization of atherosclerotic lesions, reduction in inflammatory stimuli, and prevention, slowed progression, or regression of atherosclerotic lesions (pleiotropic effects). Cellular experiments suggest that statins have an impact on endothelial function by preventing oxidized LDL-induced reduction of nitric oxide production and increased nitric oxide synthesis. Statins also impact chronic inflammation by reducing mitogen (PDGF) responsiveness, inhibiting smooth muscle cell proliferation, inhibiting monocyte chemotaxis and migration, and by reducing macrophage protease production. The absolute clinical benefit achieved may be greater in diabetic than in nondiabetic patients with CHD because diabetic patients have a higher absolute risk of recurrent CHD events and other atherosclerotic events.

IL-7-enhanced T-cell response to myelin proteins in multiple sclerosis

In this study, we investigated the in vitro proliferative response of peripheral blood T lymphocytes from MS patients and controls to MBP and MOG either in the absence or in the presence of the conditioning factor IL-7. In the absence of IL-7, T-cell reactivity to MOG and MBP was similar in MS patients and controls even if an increased MBP response was found in a subgroup of patients with active disease. In the presence of IL-7, increased T-cell reactivity to MBP was observed in MS patients suggesting that their MBP-specific T cells are in a different functional state.

[Sweet syndrome in a female patient with intestinal multiple lipomas and diverticular disease of the colon]

Sweet's syndrome (SS), or acute febrile neutrophilic dermatosis, is a condition characterized by the sudden onset of fever, leukocytosis, and painful, erythematous, well-demarcated papules and plaques which show dense, neutrophilic infiltrates on histologic examination. Myalgias and arthralgias are common. Although it may occur in the absence of other known disease, SS is often associated with hematologic disease (including leukemia), and immunologic disease (rheumatoid arthritis, inflammatory bowel disease). A case of SS is reported. Furthermore the patient presented multiple intestinal lipomas and diverticular colon disease. The authors, on the ground of recent studies which correlate SS with several digestive system disorders, hypothesize an association between acute febrile neutrophilic dermatosis and patient's intestinal diseases. Treatment with systemic corticosteroids is usually successful.

Group B Streptococcus induces apoptosis in macrophages

Group B Streptococcus (GBS) is a pathogen that has developed some strategies to resist host immune defenses. Because phagocytic killing is an important pathogenetic mechanism for bacteria, we investigated whether GBS induces apoptosis in murine macrophages. GBS type III strain COH31 r/s (GBS-III) first causes a defect in cell membrane permeability, then at 24 h, apoptosis. Apoptosis was confirmed by several techniques based on morphological changes and DNA fragmentation. Cytochalasin D does not affect apoptosis, suggesting that GBS-III needs not be within the macrophage cytoplasm to promote apoptosis. Inhibition of host protein synthesis prevents apoptosis, whereas inhibition of caspase-1 or -3, does not. Therefore, GBS can trigger an apoptotic pathway independent of caspase-1 and -3, but dependent on protein synthesis. Inhibition of apoptosis by EGTA and PMA, and enhancement of apoptosis by calphostin C and GF109203X suggests that an increase in the cytosolic calcium level and protein kinase C activity status are important in GBS-induced apoptosis. Neither alteration of plasma membrane permeability nor apoptosis were induced by GBS grown in conditions impeding hemolysin expression or when we used dipalmitoylphosphatidylcholine, which inhibited GBS beta-hemolytic activity, suggesting that GBS beta-hemolysin could be involved in apoptosis. beta-Hemolysin, by causing membrane permeability defects, could allow calcium influx, which initiates macrophage apoptosis. GBS also induces apoptosis in human monocytes but not in tumor lines demonstrating the specificity of its activity. This study suggests that induction of macrophage apoptosis by GBS is a novel strategy to overcome host immune defenses.

In vitro effects of meropenem and imipenem/cilastatin on some functions of human natural effector cells

Meropenem, a new carbapenem antibiotic, was assessed to evaluate its effects on some functional parameters of human polymorphonuclear (PMN) and natural killer (NK) cells in comparison with imipenem/cilastatin. Both drugs significantly inhibited PMN phagocytosis and chemotaxis at concentrations of 2,000 and 4,000 microg/ml. They affected PMN microbicidal activity, evaluated against Candida albicans, only at 4,000 microg/ml. A study of the effects of both drugs on peripheral NK populations and the human NK line (NK-92) showed that even at 4,000 microg/ml there was no effect on antitumor activity. These data indicate that meropenem can reduce some PMN antimicrobial functions only at very high concentrations like imipenem/cilastatin, whereas no concentration influenced NK activity.

Scintigraphic evaluation of gastroesophageal reflux in newborns

OBJECTIVES

This study was carried out to verify whether during neonatal stage gastroesophageal scintigraphy, may be useful not only to diagnose gastroesophageal reflux (GER), but also to detect pulmonary aspiration, at times responsible for respiratory symptoms frequently associated with GER.

PATIENTS AND METHODS

Gastroesophageal scintigraphy was performed on 50 newborns admitted to NICU of Brindisi in the last two years who presented symptoms as cyanosis, apnoea, bradycardia, laringeal stridor, wheezing, not related to respiratory or cardiac problems, but suspected to be clinical suggestive symptoms of "pathological" GER. After administration of 99mTC mixed with the usual meal formula, we obtained a recording period of 60-90 minutes and a later recording at 4 and 24 hours to document radioactive material in lungs.

RESULTS

Scintigraphy showed GER in 40/50 cases and despite frequent observation of respiratory symptoms (39/40 cases) in these newborns never radiation in pulmonary fields.

CONCLUSIONS

Our results could indicate that scintigraphy, noninvasive and low in radiation, may be considered effective and reliable to diagnose GER in newborns. The absence of radiation in pulmonary fields could indicate that respiratory symptoms frequently associated with GER could depend on involuntary mechanism of vagal type and not on pulmonary aspiration.