529 research outputs found
ATLAS Open Data to engage the public in Education and Research
No full textATLAS Open Data is an initiative aimed at making the data, simulations, and documentary resources of the experiment accessible to a wide audience, in accordance with the CERN Open Data policy. The project has seen the release of numerous datasets of proton-proton collisions at center-of-mass energies of 8 TeV and 13 TeV collected at the LHC during Run-1 and Run-2, allowing for the investigation of typical phenomena in high-energy physics. To facilitate their dissemination, the data are shared in accessible and commonly used formats. Additionally, they are accompanied by software and web interfaces designed for easy use, without the need for installation or coding by the user. The objective is twofold. On the one hand, the goal is to promote these activities in outreach and educational contexts, such as Summer Schools, Masterclasses, university projects, as well as various initiatives within the ATLAS Collaboration itself. On the other hand, high-energy physics
research becomes accessible to an interdisciplinary audience, involving experts from other fields to benefit from their expertise, such as machine learning and computer
science. This work provides an overview of the ATLAS Open Data resources, with concrete examples of how they can be used to promote scientific education and research in the field of particle physics
Phosphoinositide-phospholipase C beta1 mono-allelic deletion is associated with myelodysplastic syndromes evolution into acute myeloid leukemia.
No full textPurpose To evaluate the association between the presence of phosphoinositide-phospholipase C β1 (PI-PLCβ1) mono-allelic deletion with the clinical outcome of myelodysplastic syndromes (MDS) patients.
Methods PI-PLCβ1, PI-PLCβ4, and PI-PLCγ1 cytogenetic investigations were performed on 80 newly diagnosed MDS patients (18 low risk, 26 intermediate 1, 18 intermediate 2, 18 high risk) comparing the results with the clinical outcome of the patients. Moreover, fluorescent in situ hybridization results were validated by real-time polymerase chain reaction (PCR). Finally, PI-PLCβ1 gene and protein expression were assessed by both real-time PCR and immunocytochemical experiments.
Results Collectively, 35 (43.75%) of 80 of the MDS patients showed a specific mono-allelic deletion of PI-PLCβ1. Kaplan-Meier analysis revealed a significant association (P < .0001) between the PI-PLCβ1 mono-allelic deletion and a higher risk of evolution into acute myeloid leukemia (AML), since 23 of 35 MDS patients (65.7%) bearing the PI-PLCβ1 mono-allelic deletion evolved into AML. Even in multivariate analysis, the PI-PLCβ1 mono-allelic deletion retained a higher significance, with a P < .001, as a prognostic factor of evolution into AML (odds ratio [OR] 1.83; 95% CI, 2.26 to 17.24; P = .00045). Finally, PI-PLCβ1 deletion was related to an altered gene and protein expression.
Conclusion PI-PLCβ1 mono-allelic deletion is associated with a worse clinical outcome in MDS patients, hinting at the identification of a new group at higher risk of AML evolution and representing a reliable prognostic tool. Moreover, targeting PI-PLCβ1 pathways might emerge as a new therapeutic strategy for MDS
C033 Quantification of phosphoinositidephospholipase C (PI-PLC) beta 1 gene promoter methylation predicts the responsiveness to azacitidine in myelodysplastic syndromes
No full textEpigenetic Regulation of Nuclear PI-PLCbeta1 Signalling Pathway in Low-Risk MDS Patients During Azacitidine Treatment
No full textPhosphoinositide-phospholipase C (PI-PLC) beta1 can be considered a specific target for demethylating therapy in high-risk myelodysplastic syndrome (MDS) patients, as azacitidine treatment has been associated with a PI-PLCbeta1-specific promoter demethylation, and induction of PI-PLCbeta1 gene and protein expression. However, little is known about the molecular effect of azacitidine in low-risk MDS or the functional mechanisms linked with azacitidine effect on PI-PLCbeta1 promoter. In the present study, we further investigated the role of epigenetic regulation of PI-PLCbeta1, mainly focusing on the structure of the PI-PLCbeta1 promoter. We first examined the effect of azacitidine on PI-PLCbeta1 promoter methylation and gene expression in low-risk MDS. Moreover, we studied the expression of key molecules associated with the nuclear inositide signaling pathways, such as cyclin D3. By applying a chromatin immunoprecipitation method, we also studied the correlation between the demethylating effect of azacitidine and the degree of recruitment to PI-PLCbeta1 promoter of some transcription factors implicated in hematopoietic stem cell proliferation and differentiation, as well as of the methyl-CpG-binding domain proteins, which specifically interact with methylated DNA. Taken together, our results hint at a specific involvement of PI-PLCbeta1 in epigenetic mechanisms, and are particularly consistent with the hypothesis of a role for PI-PLCbeta1 in azacitidine-induced myeloid differentiation
Clonal activation of Akt in low-risk MDS patients with del(5q) treated with lenalidomide
No full textBackground: The activation of inositide signalling pathways, such as
Akt/mTOR, has been demonstrated in high-risk MDS. Akt also binds
PI-PLCgamma1, leading to a deregulation of stem cell proliferation,
differentiation and apoptosis. These processes are critical in low-risk
MDS, that usually show a marked apoptosis and a low proliferation
rate, which can be rapidly reversed, thus leading to a worse clinical
status.
Introduction: Lenalidomide is currently used in the treatment of
del(5q) low-risk MDS patients, where it may suppress the del(5q)
clone and restore a normal erythropoiesis. Lenalidomide also shows
anti-angiogenic activity and suppresses inflammatory cytokine release.
The exact molecular mechanisms underlying the effect of
Lenalidomide in MDS cells are still unclear, even though it has been
demonstrated that in Lenalidomide-sensitive del(5q) cell lines, Akt
phosphorylation is inhibited.
Purpose: We studied the effect of Lenalidomide on nuclear inositide
signalling pathways in del(5q) low-risk MDS.
Materials and Methods: We studied the expression of inositide signalling
molecules in 6 patients diagnosed with del(5q) MDS (IPSS:
Low or Int-1) who were given Lenalidomide. Given the limited number
of cells, we quantified the expression of Akt and PI-PLCgamma1
in bone marrow total mononuclear cells. As for Akt phosphorylation,
we analyzed its localization along with RPS14, in order to specifically
detect the del(5q) clone. Moreover, by Real-Time PCR analyses, we
assessed the expression of Beta-Globin, to evaluate the effect of the
drug on erythropoiesis.
Results: In our case series, 4 out of 6 del(5q) low-risk MDS patients
responded to Lenalidomide and showed an activation of erythropoiesis,
in that Beta-Globin levels increased, as compared with
baseline. Moreover, these subjects also displayed an activation of PIPLCgamma1
and Akt. Interestingly, Akt resulted to be specifically
phosphorylated in cells not showing the 5q deletion, hinting at a
clonal activation of this pathway. The 2 non responder patients early
discontinued Lenalidomide for adverse events, and for these patients
neither a clinical assessment of Lenalidomide effect, nor a molecular
analysis, were possible.
Conclusions: Our data show Akt/PI-PLCgamma1 activation during
Lenalidomide treatment, and confirm the activation of erythropoiesis in responder patients. In addition, our results indicate that Akt is
specifically phosphorylated in the 5q+ clone. Therefore, it is conceivable
that Lenalidomide strengthens the proliferation of the 5q+ clone,
whilst the del(5q) clone undergoes an apoptotic process, allowing the
restoration of the normal erythropoiesis. This is extremely important,
not only for MDS pathogenesis, but also for the development of innovative
targeted therapies
Automating cell counting in fluorescent microscopy through deep learning with c-ResUnet
No full textCounting cells in fluorescent microscopy is a tedious, time-consuming task that researchers have to accomplish to assess the effects of different experimental conditions on biological structures of interest. Although such objects are generally easy to identify, the process of manually annotating cells is sometimes subject to fatigue errors and suffers from arbitrariness due to the operator’s interpretation of the borderline cases. We propose a Deep Learning approach that exploits a fully-convolutional network in a binary segmentation fashion to localize the objects of interest. Counts are then retrieved as the number of detected items. Specifically, we introduce a Unet-like architecture, cell ResUnet (c-ResUnet), and compare its performance against 3 similar architectures. In addition, we evaluate through ablation studies the impact of two design choices, (i) artifacts oversampling and (ii) weight maps that penalize the errors on cells boundaries increasingly with overcrowding. In summary, the c-ResUnet outperforms the competitors with respect to both detection and counting metrics (respectively, F1 score = 0.81 and MAE = 3.09). Also, the introduction of weight maps contribute to enhance performances, especially in presence of clumping cells, artifacts and confounding biological structures. Posterior qualitative assessment by domain experts corroborates previous results, suggesting human-level performance inasmuch even erroneous predictions seem to fall within the limits of operator interpretation. Finally, we release the pre-trained model and the annotated dataset to foster research in this and related fields
EFFECT OF LENALIDOMIDE ON INOSITIDE-DEPENDENT SIGNAL TRANSDUCTION PATHWAYS
No full textLenalidomide (Len) has proven effectiveness in 70-80% of low-risk
MDS cases with del(5q), resulting in transfusion-independence, and
inducing a rise hemoglobin levels, suppression of the 5q clone and
improvement of bone marrow morphologic features. In del(5q) MDS,
Len might suppress the dysplastic clone, while in non-del(5q) it may
promote effective erythropoiesis, via activation of EPO signalling, which
in turn is associated with PI-PLCgamma1 pathway. However, the exact
molecular mechanisms underlying the effect of Len in MDS cells are
still unclear. Interestingly, Len targets the phosphatase PP2A, whose
gene is located in the common deleted region and which usually targets Akt. Indeed, Akt-dependent pathways are critical in low-risk MDS,
which display a marked apoptosis and a low proliferation rate. Recently,
our group showed that inositide signalling pathways are involved in
the MDS progression to AML. In particular, we demonstrated not only
that MDS can show alterations on PI-PLCbeta1 and Akt pathways, but
also that Akt is inversely correlated with PI-PLCbeta1, therefore affecting
MDS cell survival and differentiation. Here, we report on a patient
affected by MDS who was successfully treated with Len. The patient,
a 58-year old female, was diagnosed with Refractory Anemia (IPSS:
Low) and was given only supportive care before undergoing Len treatment.
Shortly after the beginning of the therapy, in 2009, the patient
showed a clinical favorable response to Len, and subsequently achieved
complete hematologic and cytogenetic remission. To assess the molecular
effects of Len on inositide signalling pathways, we analyzed the
expression of critical genes involved in cell proliferation and differentiation,
i.e. PI-PLCbeta1 and its downstream target Cyclin D3, as well as
PI-PLCgamma1, which is linked with EPO signalling and Akt activation.
That is why ongoing analyses are also trying to examine the effect
of Len on Akt, and the correlation between Len and the expression of
other genes specifically associated with erythropoiesis, like Globin
genes. So far, our results indicate that both PI-PLCbeta1 and Cyclin D3
are not significantly affected by Len, whereas PI-PLCgamma1 is specifically
induced. Consequently, these findings hint at a specific activation
of PI-PLCgamma1 signalling following Len treatment, and possibly pave
the way to further investigations aiming to better understand the role
of these pathways in the mechanism of action of Len in del(5q) MDS
Role of inositide signalling regulation in higher-risk MDS patients during epigenetic therapy
No full textBackground: Inositide signalling pathways are involved in cell
growth, differentiation and apoptosis and play a role in
the progression of myelodysplastic syndromes (MDS) towards
acute myeloid leukemia (AML). The combination of the DNA
methyltransferase inhibitor azacitidine (AZA) and the HDAC inhibitor
valproic acid (VPA) in patients with IPSS intermediate-2/high-risk
MDS has been demonstrated to be active and associated with a high
response rate in patients with MDS and unfavourable prognosis
(Voso MT et al, 2009).
Introduction: In the last few years, our group demonstrated not
only that phosphoinositide-phospholipase C beta1 (PI-PLCbeta1)
promoter gene is hyper-methylated in higher-risk MDS, but also that is affected by epigenetic therapy (Follo MY et al, PNAS 2009; Follo
MY et al. Leukemia 2010). Indeed, AZA, alone or in combination with
VPA was able to induce PI-PLCbeta1 demethylation and expression.
Purpose: In this study we further investigated the role of lipid
signalling pathways during epigenetic therapy, focusing on the
functional effect of AZA and VPA on PI-PLCbeta1 promoter in highrisk
MDS patients.
Materials and Methods: The study included 20 higher-risk MDS
patients (IPSS risk: intermediate-2 or high): 8 of them were treated
with AZA alone (75 mg/m2/day SC for 7 days/28 days), whereas 6 of
them received the combination of AZA with VPA (600–1500 mg/daily
orally) and the remaining 6 were treated only with best supportive
care. For each patient we analyzed the effect of epigenetic therapy
in correlation to PI-PLCbeta1 signalling, by analyzing the binding
affinity of transcription factors correlated to hematopoietic stem
cell differentiation and proliferation, as well as by quantifyng the
expression of molecules involved in the epigenetic machinery, such
as Class I HDACs.
Results: 8/20 (40%) of our MDS patients showed a favourable
hematologic response to epigenetic therapy and an increase in PIPLCbeta1
expression, as compared with the pre-treatment period,
thus confirming the involvement of this molecule in response
to demethylating agents. Moreover, MDS patients responding to
epigenetic treatment seem to involve the recruitment of specific
transcription factors on PI-PLCbeta1 promoter during the regulation
of methylation processes. Taken together, our data are consistent
with the hypothesis of a correlation between epigenetic treatment
and PI-PLCbeta1 signalling, thus hinting at a role for PI-PLCbeta1 in
monitoring the efficacy of epigenetic therapy and paving the way
for the development of innovative therapeutic strategies in MD
AZACITIDINE FOR HIGH RISK MYELODYSPLASTIC SYNDROMES. RETROSPECTIVE EVALUATION OF TWO DIFFERENT DOSING SCHEDULES
No full textAzacitidine (AZA) has proven effective (response rate: 60-80%) in
myelodysplastic syndromes (MDS). The currently approved AZA regimen
(AZA 7) is 75 mg/sqm/die subcutaneously (SC) for 7 days every 28
days. Recently a different AZA dosing schedule (AZA 5-2-5: 50 mg/m2/d
subcutaneously for 5 days, followed by 2 days no treatment, then 50
mg/m2/d for 5 days), which avoids week-end dosing, has shown to
induce therapeutic responses consistent with the currently approved
schedule, in a population of mainly low risk pts (Lyons, 2009). These data
prompted us to investigate the therapeutic effect of the AZA 5-2-5 regimen
in high risk MDS pts (IPSS risk: high or intermediate-2). From September
2004, in our Institution, 28 high risk MDS pts. were treated with
2 different AZA dosing schedules. Group 1 (9 pts, 8 males, median age:
68, range 60-84 yrs) received the AZA 7 regimen, while group 2 (19 pts,
13 males, median age: 69, range 37-81 yrs) received the 5-2-5 AZA regimen.
Moreover, as our group (Follo, 2009) demonstrated that phosphoinositide-phospholipase
C (PI-PLC) beta1 may represent a target for
AZA, we quantified the degree of PI-PLCbeta1 methylation and gene
expression before and during AZA administration in both groups. Pts of
group 1 received a median number of 12 (1-59) AZA cycles. Among the
8 evaluable pts (i.e.: at least 6 cycles) 5 (62.5%) showed a favourable
response, following IWG criteria (Cheson, 2006): 1 Complete Remission
(CR), 1 Partial Remission (PR) and 3 Hematologic Improvement
(HI). 3 pts died because of evolution into Acute Myeloid Leukemia
(AML), and 4 pts for other causes. One pts, still alive and under imatinib
therapy, developed Ph1+ Chronic Myeloid Leukemia (CML) after 59
courses of AZA. Mean follow-up of group 1 pts: 31 (13-79) months. Pts
of group 2 received a median number of 8 (1-17) AZA cycles. Among the
15 evaluable pts, 13 (86.6%) showed a favourable response: 5 CR
(33.3%) and 8 HI. 3 pts died because of evolution into AML, and 2 for
other causes. 2 pts underwent allogeneic stem cell transplantation, both
after achieving CR. 12 pts are alive, 9 of them still under AZA treatment. Mean follow-up of group 2 pts: 14 (1-35) months. PI-PLCbeta1 methylation
and gene expression appeared to be related to the therapeutic
response, but not to the dose schedule. Our results, although larger studies
are required, seem to confirm the effectiveness of the more convenient
AZA 5-2-5 regimen, even in high risk MDS
Epigenetic regulation of nuclear PI-PLCbeta1 signaling pathway in low-risk MDS patients during azacitidine treatment.
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