Classifying flow cytometry data using Bayesian analysis helps to distinguish ALS patients from healthy controls

Introduction

Given its wide availability and cost-effectiveness, multidimensional flow cytometry (mFC) became a core method in the field of immunology allowing for the analysis of a broad range of individual cells providing insights into cell subset composition, cellular behavior, and cell-to-cell interactions. Formerly, the analysis of mFC data solely relied on manual gating strategies. With the advent of novel computational approaches, (semi-)automated gating strategies and analysis tools complemented manual approaches.

Methods

Using Bayesian network analysis, we developed a mathematical model for the dependencies of different obtained mFC markers. The algorithm creates a Bayesian network that is a HC tree when including raw, ungated mFC data of a randomly selected healthy control cohort (HC). The HC tree is used to classify whether the observed marker distribution (either patients with amyotrophic lateral sclerosis (ALS) or HC) is predicted. The relative number of cells where the probability q is equal to zero is calculated reflecting the similarity in the marker distribution between a randomly chosen mFC file (ALS or HC) and the HC tree.

Results

Including peripheral blood mFC data from 68 ALS and 35 HC, the algorithm could correctly identify 64/68 ALS cases. Tuning of parameters revealed that the combination of 7 markers, 200 bins, and 20 patients achieved the highest AUC on a significance level of p < 0.0001. The markers CD4 and CD38 showed the highest zero probability. We successfully validated our approach by including a second, independent ALS and HC cohort (55 ALS and 30 HC). In this case, all ALS were correctly identified and side scatter and CD20 yielded the highest zero probability. Finally, both datasets were analyzed by the commercially available algorithm 'Citrus', which indicated superior ability of Bayesian network analysis when including raw, ungated mFC data.

Discussion

Bayesian network analysis might present a novel approach for classifying mFC data, which does not rely on reduction techniques, thus, allowing to retain information on the entire dataset. Future studies will have to assess the performance when discriminating clinically relevant differential diagnoses to evaluate the complementary diagnostic benefit of Bayesian network analysis to the clinical routine workup.

Improvements in Walking Distance during Nusinersen Treatment - A Prospective 3-year SMArtCARE Registry Study

BACKGROUND AND OBJECTIVES

Disease progression in patients with spinal muscular atrophy (SMA) has changed dramatically within the past years due to the approval of three different disease-modifying treatments. Nusinersen was the first drug to be approved for the treatment of SMA patients. Clinical trials provided data from infants with SMA type 1 and children with SMA type 2, but there is still insufficient evidence and only scarcely reported long-term experience for nusinersen treatment in ambulant patients. Here, we report data from the SMArtCARE registry of ambulant patients under nusinersen treatment with a follow-up period of up to 38 months.

METHODS

SMArtCARE is a disease-specific registry in Germany, Austria and Switzerland. Data are collected as real-world data during routine patient visits. Our analysis included all patients under treatment with nusinersen able to walk independently before start of treatment with focus on changes in motor function.

RESULTS

Data from 231 ambulant patients were included in the analysis. During the observation period, 31 pediatric walkers (27.2%) and 31 adult walkers (26.5%) experienced a clinically meaningful improvement of≥30 m in the 6-Minute-Walk-Test. In contrast, only five adult walkers (7.7%) showed a decline in walking distance≥30 m, and two pediatric walkers (1.8%) lost the ability to walk unassisted under treatment with nusinersen. HFMSE and RULM scores improved in pediatric and remained stable in adult patients.

CONCLUSION

Our data demonstrate a positive effect of nusinersen treatment in most ambulant pediatric and adult SMA patients. We not only observed a stabilization of disease progression or lack of deterioration, but clinically meaningful improvements in walking distance.

Interleukin-17 and Th17 Lymphocytes Directly Impair Motoneuron Survival of Wildtype and FUS-ALS Mutant Human iPSCs

Amyotrophic lateral sclerosis (ALS) is a progressive disease leading to the degeneration of motor neurons (MNs). Neuroinflammation is involved in the pathogenesis of ALS; however, interactions of specific immune cell types and MNs are not well studied. We recently found a shift toward T helper (Th)1/Th17 cell-mediated, pro-inflammatory immune responses in the peripheral immune system of ALS patients, which positively correlated with disease severity and progression. Whether Th17 cells or their central mediator, Interleukin-17 (IL-17), directly affects human motor neuron survival is currently unknown. Here, we evaluated the contribution of Th17 cells and IL-17 on MN degeneration using the co-culture of iPSC-derived MNs of fused in sarcoma (FUS)-ALS patients and isogenic controls with Th17 lymphocytes derived from ALS patients, healthy controls, and multiple sclerosis (MS) patients (positive control). Only Th17 cells from MS patients induced severe MN degeneration in FUS-ALS as well as in wildtype MNs. Their main effector, IL-17A, yielded in a dose-dependent decline of the viability and neurite length of MNs. Surprisingly, IL-17F did not influence MNs. Importantly, neutralizing IL-17A and anti-IL-17 receptor A treatment reverted all effects of IL-17A. Our results offer compelling evidence that Th17 cells and IL-17A do directly contribute to MN degeneration.

Efficacy of Retreatment After Failed Direct-acting Antiviral Therapy in Patients With HCV Genotype 1-3 Infections

Hepatitis C virus infection is causing chronic liver disease, cirrhosis, and hepatocellular carcinoma. By combining direct-acting antivirals (DAAs), high sustained virologic response rates (SVRs) can be achieved. Resistance-associated substitutions (RASs) are commonly observed after DAA failure, and especially nonstructural protein 5A (NS5A) RASs may impact retreatment options.^1-3 Data on retreatment of DAA failure patients using first-generation DAAs are limited.^4-7 Recently, a second-generation protease- and NS5A-inhibitor plus sofosbuvir (voxilaprevir/velpatasvir/sofosbuvir [VOX/VEL/SOF]) was approved for retreatment after DAA failure.⁸ However, this and other second-generation regimens are not available in many resource-limited countries or are not reimbursed by regular insurance, and recommendations regarding the selection of retreatment regimens using first-generation DAAs are very important. This study aimed to analyze patients who were re-treated with first-generation DAAs after failure of a DAA combination therapy.

[New treatments for spinal muscular atrophy]

5‑q-associated spinal muscular atrophy (SMA) has so far been a causally untreatable disease, which leads to severe, progressive physical restrictions due to the loss of spinal motor neurons. However, the monogenetic cause of the relatively short coding "survival motor neuron" (SMN) 1 gene sequence and the presence of almost identical gene copies, the SMN2 genes, offer favorable conditions for the development of new therapeutic approaches. While previously only supportive and palliative therapies could be used, new disease-modifying drugs are now available for the first time. Nusinersen, an antisense oligonucleotide (ASO), is the first drug that has received approval in Germany to treat SMA. Further therapeutic approaches such as the so-called "small molecules" or the gene replacement therapy are currently still being tested in clinical studies or are already waiting for approval by the European Medicines Agency (EMA). In this article, the most important disease-modifying drugs of SMA, the associated studies and their challenges are presented.

Peripheral proinflammatory Th1/Th17 immune cell shift is linked to disease severity in amyotrophic lateral sclerosis

Neuroinflammation is involved in the pathogenesis of amyotrophic lateral sclerosis (ALS), but only limited data are available on systematic peripheral and central immune cell profiles in ALS. We studied detailed immune profiles of 73 ALS patients and 48 healthy controls (controls) in peripheral blood by fluorescence-activated cell sorting as well as cytokine expression profiles in serum. In a subgroup of 16 ALS patients and 10 controls we additionally studied cerebrospinal fluid (CSF) samples. In peripheral blood, T cell subtypes presented a shift towards pro-inflammatory Th 1 and Th 17 cells whereas anti-inflammatory Th2 and T regulatory cells were decreased. Important players in innate immunity including distinct monocyte (Mo) and natural killer (NK) cell subtypes were changed in ALS patients compared to controls. Pro-inflammatory serum cytokines such as interleukin (IL)-1 beta, IL-6 and interferon-gamma (IFN-gamma) were increased and the anti-inflammatory cytokine IL-10 was decreased. Correlation analysis revealed moderate negative correlations between Th1 and Th17 to the ALS functional rating scale revised (ALSFRS-R) and to forced vital capacity. In CSF samples, no relevant alteration of the immune profile was found. In conclusion, the immune profile in ALS was shifted towards a Th1/Th17 cell-mediated pro-inflammatory immune response and correlated to disease severity and progression. Large prospective studies are needed to confirm these findings.

Phenotypes and malignancy risk of different FUS mutations in genetic amyotrophic lateral sclerosis

OBJECTIVE

Mutations in Fused in Sarcoma (FUS or TLS) are the fourth most prevalent in Western European familial amyotrophic lateral sclerosis (ALS) populations and have been associated with causing both early and very late disease onset. FUS aggregation, DNA repair deficiency, and genomic instability are contributors to the pathophysiology of FUS-ALS, but their clinical significance per se and their influence on the clinical variability have yet to be sufficiently investigated. The aim of this study was to analyze genotype-phenotype correlations and malignancy rates in a newly compiled FUS-ALS cohort.

METHODS

We cross-sectionally reviewed FUS-ALS patient histories in a multicenter cohort with 36 novel cases and did a meta-analysis of published FUS-ALS cases reporting the largest genotype-phenotype correlation of FUS-ALS.

RESULTS

The age of onset (median 39 years, range 11-80) was positively correlated with the disease duration. C-terminal domain mutations were found in 90%. Among all, P525L and truncating/ frameshift mutations most frequently caused juvenile onset, rapid disease progression, and atypical ALS often associated with negative family history while the R521 mutation site was associated with late disease onset and pure spinal phenotype. Malignancies were found in one of 40 patients.

INTERPRETATION

We report the largest genotype-phenotype correlation of FUS-ALS, which enables a careful prediction of the clinical course in newly diagnosed patients. In this cohort, FUS-ALS patients did not have an increased risk for malignant diseases.

Vergleich der Befunde von 18-FDG- PET und CT beim prätherapeutischen Staging maligner Lymphome

Ziel: Vergleich der diagnostischen Aussagekraft von FDG-PET und CT zum Staging vor Therapie unter Berücksichtigung von Lokalisation, Durchmesser und Histologie der Läsion sowie Erfassung des FDG-Uptakes. Methoden: CT- und FDG-PET-Untersuchungen bei 27 Patienten mit histologisch gesichertem malignen Lymphom als Erstmanifestation oder Rezidiv wurden retrospektiv und unabhängig voneinander ausgewertet. CT-positive nodale Läsionen waren im Querdurchmesser (DCT) >15 mm. Bei visueller Auswertung in iterativ rekonstruierten PET-Studien gefundene fokale, unphysiologische FDG-Speicherungen wurden positiv gewertet und hinsichtlich Läsionsgröße (DPET) und partial-volumenkorrigierten standardisierten Uptake-Werten (SUV) quantifiziert. Eine Unterteilung der Läsionen erfolgte nach Histologie und Qualität (abgrenzbarer Lymphknoten, Konglomerattumor, extranodale Läsion). Ergebnis: CT beschrieb bei 26 Patienten 78 Läsionen, alle auch durch PET bestätigt. PET lokalisierte darüber hinaus weitere 18 Läsionen (+23%), bei hochmalignen Non-Hodgkin-Lymphomen (NHL) sogar +25%. Im Bereich des Halses sowie bei Lungenläsionen waren die Verfahren gleichwertig, bei der Beurteilung der übrigen Lymphknotenregionen sowie von Leber und Milz wies PET mehr Läsionen nach. Der SUV war bei hochmalignen NHL (19,0) signifikant höher als bei niedrigmalignen NHL und M. Hodgkin (10,6 bzw. 11,1). DCT und DPET korrelierten bei abgrenzbaren Lymphknoten signifikant (r = 0,75). Schlußfolgerung: FDG-PET ist der CT im Staging maligner Lymphome vor Therapie ebenbürtig bis überlegen. Hierzu ist eine qualitative Befundung ausreichend. Die zusätzliche quantitative Auswertung kann bei NHL einen Hinweis auf den Malignitätsgrad geben.

Real-world use, effectiveness and safety of anti-viral treatment in chronic hepatitis C genotype 3 infection

BACKGROUND

Treatment of chronic hepatitis C genotype 3 (GT3) is more challenging compared with other genotypes. Since 2014, several new treatment regimens have been approved but sometimes based on limited data.

AIM

To validate the use, effectiveness and safety of anti-viral treatment in chronic hepatitis C genotype 3 infection under real-word conditions.

METHODS

The German Hepatitis C-Registry is a large national non-interventional real-world study for patients with chronic hepatitis C. A total of 1322 GT3 patients were enrolled (211 untreated and 1111 treated patients).

RESULTS

Between February 2014 and September 2015, five different treatment strategies have been used (PegIFN+RBV, PegIFN+RBV+SOF, SOF+RBV, DCV+SOF±RBV, LDV/SOF±RBV). Treatment uptake and use of treatment concepts changed markedly and rapidly during the study influenced by new approvals, guideline recommendations, and label updates. PegIFN-based therapies constantly declined while DCV-based therapies increased with one interruption after the approval of LDV/SOF, which was frequently used until new guidelines recommended not using this combination for GT3. Per-protocol SVR ranged from 80.9% in the PegIFN+RBV group to 96.1% in PegIFN+RBV+SOF treated patients. Treatment-experienced patients with cirrhosis showed a suboptimal SVR of 68% for SOF+RBV but a high SVR of 90-95% for DCV+SOF±RBV. The safety analysis showed more adverse events and a stronger decline of haemoglobin for RBV containing regimens.

CONCLUSIONS

Real-world data can validate the effectiveness and safety for treatment regimens that had previously been approved with limited data, in particular for specific subgroups of patients. The present study demonstrates how rapid new scientific data, new treatment guidelines, new drug approvals and label changes are implemented into routine clinical practice today.

Quality of life after liver transplantation

Quality of life (QoL) is an outcome criterion of increasing importance after orthotopic liver transplantation (OLT). The background of this development is the dramatic improvement in patient survival rates over the past two decades combined with the question of the quality of this survival. Among 339 OLT performed in Kiel since 1987, 123 recipients (70 males, 53 females) of mean age 56.7 +/- 13.1 years who underwent transplantation between August 1992 and June 2007 were subjected to European Organization for Research and Treatment of Cancer (EORTC) Quality of Life Questionnaire (QLQ) C30 plus a liver transplant specific module to analyze QoL. In addition, we included 40 patients listed for OLT in the univariate and multivariate analyses performed using SPSS13.0. A cohort of healthy individuals served as the control group. QoL (global health) among liver recipients was reduced compared with the control group and improved compared with patients on the waiting list. Comparison of the underlying liver diseases showed a comparable QoL between postalcoholic cirrhosis and cholestatic liver diseases. Retransplantation was accompanied by a significant loss of QoL. Cyclosporine-treated recipients displayed a better QoL compared with those treated with tacrolimus. After establishing a system of continuous, systematic QoL assessment, we combined these results with survival outcomes. Further research must focus on advanced statistical methodology that combines these 2 major outcome parameters (QoL and survival). Furthermore, the influence of medical parameters, such of co-morbidity or immunosuppression, needs to be further established with reference to QoL.

Two germ cell lineages with genomes of different species in one and the same animal

Cytological evidence for two germ cell lineages, each with the DNA-content of one of the parental species only, was obtained for certain males of the hybridogenic water frog Rana esculenta (R. ridibunda x R. lessonae) by means of DNA flow cytometry. The approach was based on the 16 +/- 2% difference in the DNA-content of genomes of the parental species. Two types of germ cells were observed in six out of 39 males studied from populations where such males did exist. The term 'hybrid amphispermy' is proposed for the phenomenon. Occurrence of the 'hybrid amphispermy' suggests that the direction of elimination (i.e., which genome being eliminated) is determined in R. esculenta by the relative activity of putative elimination-inducing factor(s) in each of the parental genomes, which can alternate from cell to cell.

[Inflammatory reactions in the wear particle induced and infectious periprosthetic membrane of loosened hip- and knee endoprostheses: pathogenetic relevance of differentially expressed genes cd9, cd11b, cd18, cd52 and pdgfrbeta]

BACKGROUND

A previous cDNA-microarray analysis described constantly differentially expressed genes in wear particle induced and infectious SLIM (synovial-like interface membrane). This study aims to validate the cDNA microarray data in order to approve differences of the gene expression profiles of RNA and proteins.

METHODS

Tissue from 16 wear particle induced and 20 infectious periprosthetic membranes were analyzed by RT-PCR and immunohistology with regard to the expression of inflammatoric associated genes.

RESULTS

RT-PCR showed the genes cd9, cd11b, cd18, cd52 as well as pdgfrbeta in interface membranes. In the wear particle induced membrane the immunohistochemical analysis showed a significantly weaker gene expression of PDGFRbeta, whereas the differential overexpression of CD9, CD11b and CD52 was confirmed. For CD18, there was no difference in expression between wear induced and infectious periprosthetic tissue.

CONCLUSION

Different pathomechanisms, which are reflected by different gene expression profiles, might produce different types of periprosthetic membranes. By RT-PCR and immunohistochemical analysis the micro array data of the genes cd9, cd11b, cd52 and pdgfrbeta could be validated. Identifying the gene products of cd9, cd11b and cd52 in blood or tissue may help to differentiate between wear induced and infectious loosening.

Avalanche dynamics, surface roughening, and self-organized criticality: Experiments on a three-dimensional pile of rice

We present a two-dimensional system that exhibits features of self-organized criticality. The avalanches that occur on the surface of a pile of rice are found to exhibit finite size scaling in their probability distribution. The critical exponents are tau=1.21(2) for the avalanche size distribution and D=1.99(2) for the cutoff size. Furthermore, the geometry of the avalanches is studied, leading to a fractal dimension of the active sites of d(B)=1.58(2). Using a set of scaling relations, we can calculate the roughness exponent alpha=D-d(B)=0.41(3) and the dynamic exponent z=D(2-tau)=1.56(8). This result is compared with that obtained from a power-spectrum analysis of the surface roughness, which yields alpha=0.42(3) and z=1.5(1) in excellent agreement with those obtained from the scaling relations.