Showing papers by "Patrizia Rizzu published in 2020"
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Engelhardt Institute of Molecular Biology1, University of Toronto2, National University of Singapore3, University of Edinburgh4, Aalborg University – Copenhagen5, Imperial College London6, Russian Academy of Sciences7, Hiroshima University8, University of Cape Town9, McGill University10, Biotec11, University of Birmingham12, Stanford University13, ETH Zurich14, Weizmann Institute of Science15, German Center for Neurodegenerative Diseases16, Osaka University17, Johns Hopkins University18, University of Glasgow19, Karolinska Institutet20, Moscow Institute of Physics and Technology21, King Abdullah University of Science and Technology22, University of Copenhagen23, Princess Margaret Cancer Centre24, University of Udine25
TL;DR: The largest-to-date lncRNA knockdown data set with molecular phenotyping is disseminated for further exploration and functional roles for ZNF213-AS1 and lnc-KHDC3L-2 are highlighted.
Abstract: Long noncoding RNAs (lncRNAs) constitute the majority of transcripts in the mammalian genomes, and yet, their functions remain largely unknown. As part of the FANTOM6 project, we systematically knocked down the expression of 285 lncRNAs in human dermal fibroblasts and quantified cellular growth, morphological changes, and transcriptomic responses using Capped Analysis of Gene Expression (CAGE). Antisense oligonucleotides targeting the same lncRNAs exhibited global concordance, and the molecular phenotype, measured by CAGE, recapitulated the observed cellular phenotypes while providing additional insights on the affected genes and pathways. Here, we disseminate the largest-to-date lncRNA knockdown data set with molecular phenotyping (over 1000 CAGE deep-sequencing libraries) for further exploration and highlight functional roles for ZNF213-AS1 and lnc-KHDC3L-2.
97 citations
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TL;DR: An automated system with protocols suitable for routine hiPSC culture and differentiation into cortical and dopaminergic neurons is presented and is suitable for long term hands-free culture and high-content/high-throughput hiPSS-based compound, RNAi and CRISPR/Cas9 screenings to identify novel disease mechanisms and drug targets.
Abstract: Manual culture and differentiation protocols for human induced pluripotent stem cells (hiPSC) are difficult to standardize, show high variability and are prone to spontaneous differentiation into unwanted cell types. The methods are labor-intensive and are not easily amenable to large-scale experiments. To overcome these limitations, we developed an automated cell culture system coupled to a high-throughput imaging system and implemented protocols for maintaining multiple hiPSC lines in parallel and neuronal differentiation. We describe the automation of a short-term differentiation protocol using Neurogenin-2 (NGN2) over-expression to produce hiPSC-derived cortical neurons within 6‒8 days, and the implementation of a long-term differentiation protocol to generate hiPSC-derived midbrain dopaminergic (mDA) neurons within 65 days. Also, we applied the NGN2 approach to a small molecule-derived neural precursor cells (smNPC) transduced with GFP lentivirus and established a live-cell automated neurite outgrowth assay. We present an automated system with protocols suitable for routine hiPSC culture and differentiation into cortical and dopaminergic neurons. Our platform is suitable for long term hands-free culture and high-content/high-throughput hiPSC-based compound, RNAi and CRISPR/Cas9 screenings to identify novel disease mechanisms and drug targets.
21 citations
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TL;DR: This study confirms previous findings of heterozygous STUB1 mutations as the cause of SCA48 and highlights its prominent cognitive involvement, besides cerebellar ataxia and movement disorders as cardinal features.
Abstract: Objective
To describe the clinical and pathologic features of a novel pedigree with heterozygous STUB1
mutation causing SCA48.
Methods
We report a large pedigree of Dutch decent. Clinical and pathologic data were reviewed, and
genetic analyses (whole-exome sequencing, whole-genome sequencing, and linkage analysis)
were performed on multiple family members.
Results
Patients presented with adult-onset gait disturbance (ataxia or parkinsonism), combined with
prominent cognitive decline and behavioral changes. Whole-exome sequencing identified
a novel heterozygous frameshift variant c.731_732delGC (p.C244Yfs*24) in STUB1 segregating with the disease. This variant was present in a linkage peak on chromosome 16p13.3.
Neuropathologic examination of 3 cases revealed a consistent pattern of ubiquitin/p62-positive
neuronal inclusions in the cerebellum, neocortex, and brainstem. In addition, tau pathology was
present in 1 case.
Conclusions
This study confirms previous findings of heterozygous STUB1 mutations as the cause of SCA48
and highlights its prominent cognitive involvement, besides cerebellar ataxia and movement
disorders as cardinal features. The presence of intranuclear inclusions is a pathologic hallmark
of the disease. Future studies will provide more insight into its pathologic heterogeneity.
19 citations
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TL;DR: Overall, the MR study did not support the direct causal association between LTL and the ALS risk in neither population, but provided suggestive evidence for the mediation role of LDL or TC on the influence of L TL and ALS in the European population.
Abstract: We employed Mendelian randomization (MR) to evaluate the causal relationship between leukocyte telomere length (LTL) and amyotrophic lateral sclerosis (ALS) with summary statistics from genome-wide association studies (n = ~ 38,000 for LTL and ~ 81,000 for ALS in the European population; n = ~ 23,000 for LTL and ~ 4,100 for ALS in the Asian population). We further evaluated mediation roles of lipids in the pathway from LTL to ALS. The odds ratio per standard deviation decrease of LTL on ALS was 1.10 (95% CI 0.93-1.31, p = 0.274) in the European population and 0.75 (95% CI 0.53-1.07, p = 0.116) in the Asian population. This null association was also detected between LTL and frontotemporal dementia in the European population. However, we found that an indirect effect of LTL on ALS might be mediated by low density lipoprotein (LDL) or total cholesterol (TC) in the European population. These results were robust against extensive sensitivity analyses. Overall, our MR study did not support the direct causal association between LTL and the ALS risk in neither population, but provided suggestive evidence for the mediation role of LDL or TC on the influence of LTL and ALS in the European population.
5 citations
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2 citations
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01 Jan 2020
TL;DR: Gliomas overexpressing (b)HLH TFs are sensitive toward inhibition of the ATR kinase, and the combination of ATR inhibition plus temozolomide or radiation therapy in this molecular subgroup are warranted.
Abstract: Background The overexpression of (basic)helix-loop-helix ((b)HLH) transcription factors (TFs) is frequent in malignant glioma. We investigated molecular effects upon disruption of the (b)HLH network by a dominant-negative variant of the E47 protein (dnE47). Our goal was to identify novel molecular subgroup-specific therapeutic strategies. Methods Glioma cell lines LN229, LNZ308, and GS-2/GS-9 were lentivirally transduced. Functional characterization included immunocytochemistry, immunoblots, cytotoxic, and clonogenic survival assays in vitro, and latency until neurological symptoms in vivo. Results of cap analysis gene expression and RNA-sequencing were further validated by immunoblot, flow cytometry, and functional assays in vitro. Results The induction of dnE47-RFP led to cytoplasmic sequestration of (b)HLH TFs and antiglioma activity in vitro and in vivo. Downstream molecular events, ie, alterations in transcription start site usage and in the transcriptome revealed enrichment of cancer-relevant pathways, particularly of the DNA damage response (DDR) pathway. Pharmacologic validation of this result using ataxia telangiectasia and Rad3 related (ATR) inhibition led to a significantly enhanced early and late apoptotic effect compared with temozolomide alone. Conclusions Gliomas overexpressing (b)HLH TFs are sensitive toward inhibition of the ATR kinase. The combination of ATR inhibition plus temozolomide or radiation therapy in this molecular subgroup are warranted.
1 citations