MAPPING BCR-ABL1 FUSION POINTS IN CHRONIC MYELOID LEUKEMIA BY NEXT GENERATION SEQUENCING

Chronic myeloid leukemia (CML) is a myeloproliferative disorder cytogenetically characterized by a reciprocal translocation between the long arms of chromosome 9 and 22 t(9;22) that leads to the formation of the BCR-ABL1 fusion gene, coding for a deregulated tyrosine kinase with oncogenic activity. In clinical routine, mRNA amount of the chimeric transcript is considered proportional to the leukemic clone and is used for the molecular monitoring of patients. However, qRT-PCR cannot identify transcriptionally silent leukemic cells that can be present in minimal residual disease (MRD). To monitor MRD it is necessary to develop a qPCR assay on DNA sequences spanning BCR-ABL1, that are patient specific. Previous results obtained by Prof. G. Porta\u2019s group (unpublished) have demonstrated that DNA detection is positive while mRNA is not in 30% of time points, indicating the presence of transcriptionally silent cells. Breakpoints in these patients were characterized by laborious long-range PCR and cloning not suitable for a clinical application. To overcome this limiting step we set up a DNA capturing assay to target all kind of breakpoints that give rise to different BCR-ABL1 transcripts. Captured regions were then sequenced with a next generation protocol. The idea was to use the identified patient specific breakpoints to setup qPCR assays to monitor MRD. We successfully identified BCR-ABL1 fusion points in 9 over 10 samples, with single nucleotide accuracy, by setting up a bioinformatics workflow specifically developed for this purpose. All findings were validated with Sanger sequencing. This project was performed in collaboration with Prof. Giovanni Porta of University of Insubria

A bayesian nonparametric model for white blood cells in patients with lower urinary tract symptoms

Lower Urinary Tract Symptoms (LUTS) affect a significant proportion of the population and often lead to a reduced quality of life. LUTS overlap across a wide variety of diseases, which makes the diagnostic process extremely complicated. In this work we focus on the relation between LUTS and Urinary Tract Infection (UTI). The latter is detected through the number of White Blood Cells (WBC) in a sample of urine: WBC≥ 1 indicates UTI and high levels may indicate complications. The objective of this work is to provide the clinicians with a tool for supporting the diagnostic process, deepening the available knowledge about LUTS and UTI. We analyze data recording both LUTS profile and WBC count for each patient. We propose to model the WBC using a random partition model in which we specify a prior distribution over the partition of the patients which includes the clustering information contained in the LUTS profile. Then, within each cluster, the WBC counts are assumed to be generated by a zero-inflated Poisson distribution. The results of the predictive distribution allows to identify the symptoms configuration most associated with the presence of UTI as well as with severe infections

Lower urinary tract symptoms that predict microscopic pyuria

INTRODUCTION AND HYPOTHESIS: Urinary dipsticks and culture analyses of a mid-stream urine specimen (MSU) at 10(5) cfu ml(-1) of a known urinary pathogen are considered the gold standard investigations for diagnosing urinary tract infection (UTI). However, the reliability of these tests has been much criticised and they may mislead. It is now widely accepted that pyuria (≥1 WBC μl(-1)) detected by microscopy of a fresh unspun, unstained specimen of urine is the best biological indicator of UTI available. We aimed to scrutinise the greater potential of symptoms analysis in detecting pyuria and UTI. METHODS: Lower urinary tract symptom (LUTS) descriptions were collected from patients with chronic lower urinary tract symptoms referred to a tertiary referral unit. The symptoms informed a 39-question inventory, grouped into storage, voiding, stress incontinence and pain symptoms. All questions sought a binary yes or no response. A bespoke software package was developed to collect the data. The study was powered to a sample of at least 1,990 patients, with sufficient power to analyse 39 symptoms in a linear model with an effect size of Cohen's f(2) = 0.02, type 1 error probability = 0.05; and power (1-β); 95% where β is the probability of type 2 error). The inventory was administered to 2,050 female patients between August 2004 and November 2011. The data were collated and the following properties assessed: internal consistency, test-retest reliability, inter-observer reliability, internal responsiveness, external responsiveness, construct validity analysis and a comparison with the International Consultation on Incontinence Modular Questionnaire for female lower urinary tract symptoms (ICIQ-FLUTS). The dependent variable used as a surrogate marker of UTI was microscopic pyuria. An MSU sample was sent for routine culture. RESULTS: The symptoms proved reliable predictors of microscopic pyuria. In particular, voiding symptoms correlated well with microscopic pyuria (χ(2) = 88, df = 1, p < 0.001). The symptom inventory has significant psychometric characteristics as below: test-retest reliability: Cronbach's alpha was 0.981; inter-observer reliability, Cronbach's alpha was 0.995, internal responsiveness F = 221, p < 0.001, external responsiveness F = 359, df = 5, p < 0.001. The correlation coefficients for the domains of the ICIQ-FLUTS were around R = 0.5, p < 0.001. CONCLUSION: This symptoms score performed well on the standard, psychometric validation. The score changed in response to treatment and in a direction appropriate to the changes in microscopic pyuria. It correlated with measures of quality of life. It would seem to make a good candidate for monitoring treatment progress in ordinary clinical practice

Recalcitrant chronic bladder pain and recurrent cystitis but negative urinalysis - what should we do?

Purpose: Lower urinary tract symptoms (LUTS) may be associated with chronic urinary tract infection (UTI) undetected by routine diagnostic tests. Antimicrobial therapy might confer benefit for these patients. Materials and Methods: Over ten years, we treated patients with chronic LUTS. Pyuria was adopted as the principal biomarker of infection. Urinary leucocyte counts were recorded from microscopy of fresh midstream urine (MSU) samples. Antibiotics were prescribed and the prescription adjusted to achieve a measurable clinical response and a reduction in pyuria. Results: We treated 624 women (mean age=53.4 years; sd=18) with chronic LUTS and pyuria. The mean duration of symptoms prior to presentation was 6.5 years. Only 16% of MSU cultures submitted were positive (≥105 cfu ml-1). Mean treatment length was 383 days (SD=347; 95% CI=337-428). Treatment was associated with a reduction in total LUTS (F=98; p=.0001), 24-hour frequency (F=75; p=.0001), urinary 3 urgency (F=90; p=.0001), lower urinary tract pain (F=108; p=.0001), voiding symptoms (F=10; p=.002) and pyuria (F=15.4; p=.0001). Full-dose first-generation urinary antibiotic (such as cefalexin, nitrofurantoin, or trimethoprim) was combined with Methenamine Hippurate. We recorded 475 adverse events (AEs) during 273,762 treatment days. There was only one serious adverse event (SAE). We observed no increase in the proportion of resistant bacterial isolates. Conclusion: This large case series demonstrates that patients with chronic LUTS and pyuria experience symptom regression and a reduction in urinary tract inflammation associated with antimicrobial therapy. Disease regression was achieved with a low frequency of AEs. These results provide preliminary data to inform a future RCT

Long-term management of natalizumab discontinuation in a large monocentric cohort of multiple sclerosis patients

Background Pivotal and post-marketing studies demonstrated the impressive efficacy and the good tolerability profile of natalizumab in Multiple Sclerosis patients. On the other hand long-term safety of natalizumab therapy is burdened by the risk of progressive multifocal leukoencephalopathy, especially in anti-JCV seropositive patients treated for more than two years. Some of these patients must stop the drug at the risk of disease reactivation. Objectives To evaluate the effects of natalizumab discontinuation in a monocentric cohort of multiple sclerosis patients followed for a mean time of 22.4 months. Methods One hundred and ten patients, who stopped therapy after at least 12 infusions, were followed with periodic clinical and magnetic resonance imaging evaluations. One hundred patients started either immunomodulant therapy (n=90) or fingolimod (n=10) while 10 remained without any drug. Results "Disease-activity free" patients were 25% at one year after discontinuation and annualized relapse rate significantly increased from 0.06 to 0.84 (p<0.0001). We found that the risk of reactivation peaked despite alternative treatments between the second and the eighth month after suspension, a so-called "high risk period". During this period the majority of patients showed a return to pre-natalizumab disease activity while 10% of patients presented a "rebound activity". A higher pre-natalizumab disease activity was correlated with an increased risk of reactivation (p=0.004). Conclusions Our data suggest that disease reactivation peaked during a "high risk period" between the second and the eighth month since stopping the drug. During this period no alternative treatments seemed to provide an adequate protection from disease reactivation. Though transient, this phase could be potentially dangerous, therefore we need to develop more effective strategies to deal with this challenge

Habitats Directive in northern Italy: a series of proposals for habitat definition improvement

Habitats Directive (92/43/EEC) is the cornerstone of nature conservation in Europe and is at the core of the EU Biodiversity Strategy for 2030. There is room, however, for its improvement, at least for northern Italy, where ambiguities in the definition of habitat types of Annex I of the Habitats Directive are not novel and interpretation difficulties have been highlighted. Sharpening the characterization of habitat types represents an opportunity for lowering classification uncertainties and improving conservation success. With the aim to refine the definitions of habitat types and associated typical species of the Habitats Directive, a group of vegetation scientists of the Italian Society of Vegetation Science based in northern Italy made the exercise of finding viable proposals for those habitat types having a problematic interpretation in the Alpine biogeographical region of Italy. Such proposals arise from group discussions among scientists, and professionals, thus offering a shared view. We prepared 9 habitat proposals important for this geographic area. They include new habitat types at the European level, new subtypes within pre-existing habitat types, including some adjustments of the recently proposed subtypes with respect to northern Italy, and recognition of priority criteria for a pre-existing habitat type. With a vision of tailored conservation, our proposals represent a starting point in view of a future update of Annex I. Furthermore, the list of typical species could be useful for preparing expert systems for automatic classification. Irrespective of legally binding solutions in place, we caution these proposals represent relevant baseline conservation indications that local and regional administrations of the Alpine Arch should consider

Cystic Fibrosis Defective Response to Infection Involves Autophagy and Lipid Metabolism

Cystic fibrosis (CF) is a hereditary disease, with 70% of patients developing a proteinopathy related to the deletion of phenylalanine 508. CF is associated with multiple organ dysfunction, chronic inflammation, and recurrent lung infections. CF is characterized by defective autophagy, lipid metabolism, and immune response. Intracellular lipid accumulation favors microbial infection, and autophagy deficiency impairs internalized pathogen clearance. Myriocin, an inhibitor of sphingolipid synthesis, significantly reduces inflammation, promotes microbial clearance in the lungs, and induces autophagy and lipid oxidation. RNA-seq was performed in Aspergillusfumigatus-infected and myriocin-treated CF patients' derived monocytes and in a CF bronchial epithelial cell line. Fungal clearance was also evaluated in CF monocytes. Myriocin enhanced CF patients' monocytes killing of A. fumigatus. CF patients' monocytes and cell line responded to infection with a profound transcriptional change; myriocin regulates genes that are involved in inflammation, autophagy, lipid storage, and metabolism, including histones and heat shock proteins whose activity is related to the response to infection. We conclude that the regulation of sphingolipid synthesis induces a metabolism drift by promoting autophagy and lipid consumption. This process is driven by a transcriptional program that corrects part of the differences between CF and control samples, therefore ameliorating the infection response and pathogen clearance in the CF cell line and in CF peripheral blood monocytes

Notulae to the Italian flora of algae, bryophytes, fungi and lichens: 3

In this contribution, new data concerning bryophytes, fungi and lichens and of the Italian flora are presented. It includes new records and confirmations for the bryophyte genera Dicranodontium, Fontinalis, Lophocolea and Riccia, the fungal genus Diplolaeviopsis, the lichen genera Agonimia, Cladonia, Protoparmelia, Rhizocarpon, and Scytinium

Out-of-Hospital Cardiac Arrest in Patients With Psychiatric Disorders - Characteristics and Outcomes

Aims To investigate whether the recent improvements in pre-hospital cardiac arrest-management and survival following out-of-hospital cardiac arrest (OHCA) also apply to OHCA patients with psychiatric disorders. Methods We identified all adult Danish patients with OHCA of presumed cardiac cause, 2001–2015. Psychiatric disorders were defined by hospital diagnoses up to 10 years before OHCA and analyzed as one group as well as divided into five subgroups (schizophrenia-spectrum disorders, bipolar disorder, depression, substance-induced mental disorders, other psychiatric disorders). Association between psychiatric disorders and pre-hospital OHCA-characteristics and 30-day survival were assessed by multiple logistic regression. Results Of 27,523 OHCA-patients, 4772 (17.3%) had a psychiatric diagnosis. Patients with psychiatric disorders had lower odds of 30-day survival (0.37 95% confidence interval 0.32–0.43) compared with other OHCA-patients. Likewise, they had lower odds of witnessed status (0.75 CI 0.70–0.80), bystander cardiopulmonary resuscitation (CPR) (0.77 CI 0.72–0.83), shockable heart rhythm (0.37 95% CI, 0.33–0.40), and return of spontaneous circulation (ROSC) at hospital arrival (0.66 CI 0.59–0.72). Similar results were seen in all five psychiatric subgroups. The difference in 30-day survival between patients with and without psychiatric disorders increased in recent years: from 8.4% (CI 7.0–10.0%) in 2006 to 13.9% (CI 12.4–15.4%) in 2015 and from 7.0% (4.3–10.8%) in 2006 to 7.0% (CI 4.5–9.7%) in 2015, respectively. Conclusion Patients with psychiatric disorders have lower survival following OHCA compared to non-psychiatric patients and the gap between the two groups has widened over time

Transcriptomic analyses and leukocyte telomere length measurement in subjects exposed to severe recent stressful life events

Stressful life events occurring in adulthood have been found able to affect mood and behavior, thus increasing the vulnerability for several stress-related psychiatric disorders. However, although there is plenty of clinical data supporting an association between stressful life events in adulthood and an enhanced vulnerability for psychopathology, the underlying molecular mechanisms are still poorly investigated. Thus, in this study we performed peripheral/whole-genome transcriptomic analyses in blood samples obtained from 53 adult subjects characterized for recent stressful life events occurred within the previous 6 months. Transcriptomic data were analyzed using Partek Genomics Suite; pathway and network analyses were performed using Ingenuity Pathway Analysis and GeneMANIA Software. We found 207 genes significantly differentially expressed in adult subjects who reported recent stressful life experiences (n=21) compared with those without such experiences (n=32). Moreover, the same subjects exposed to such stressful experiences showed a reduction in leukocyte telomere length. A correlation analyses between telomere length and transcriptomic data indicated an association between the exposures to recent stressful life events and the modulation of several pathways, mainly involved in immune-inflammatory-related processes and oxidative stress, such as natural killer cell signaling, interleukin-1 (IL-1) signaling, MIF regulation of innate immunity and IL-6 signaling. Our data suggest an association between exposures to recent stressful life events in adulthood and alterations in the immune, inflammatory and oxidative stress pathways, which could be also involved in the negative effect of stressful life events on leukocyte telomere length. The modulation of these mechanisms may underlie the clinical association between the exposure to recent Stressful life events in adulthood and an enhanced vulnerability to develop psychiatric diseases in adulthood