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Article: Éosinophilie chez des patients traités par tocilizumab dans le cadre d’une polyarthrite rhumatoïde.

Vallat, Julie / Pieren-Salazar, Amara / Zenklusen, Christiane / Brulhart, Laure

2022 Volume 18, Issue 782, Page(s) 1014–1016

Abstract: Hypereosinophilia is a haematological complication that can lead to severe organ damage. This article describes 2 patients who presented eosinophilia under treatment with tocilizumab for rheumatoid arthritis. We will describe the evolution of ... ...

Title translation	Cases of eosinophilia in patients treated with Tocilizumab for rheumatoid arthritis.
Abstract	Hypereosinophilia is a haematological complication that can lead to severe organ damage. This article describes 2 patients who presented eosinophilia under treatment with tocilizumab for rheumatoid arthritis. We will describe the evolution of eosinophilia over time, with the monitoring of medication and discuss the potential link with the treatment as well as the importance of this manifestation in the context of the disease.
MeSH term(s)	Antibodies, Monoclonal, Humanized/adverse effects ; Antirheumatic Agents/adverse effects ; Arthritis, Rheumatoid/complications ; Arthritis, Rheumatoid/drug therapy ; Eosinophilia/chemically induced ; Eosinophilia/complications ; Humans ; Treatment Outcome
Chemical Substances	Antibodies, Monoclonal, Humanized ; Antirheumatic Agents ; tocilizumab (I031V2H011)
Language	French
Publishing date	2022-05-18
Publishing country	Switzerland
Document type	Journal Article
ZDB-ID	2177010-4
ISSN	1660-9379
ISSN	1660-9379
DOI	10.53738/REVMED.2022.18.782.1014
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Article ; Online: Vitamin D receptor expression is associated with improved overall survival in human glioblastoma multiforme.

Salomón, Débora G / Fermento, María E / Gandini, Norberto A / Ferronato, María J / Arévalo, Julián / Blasco, Jorge / Andrés, Nancy C / Zenklusen, Jean C / Curino, Alejandro C / Facchinetti, María M

Journal of neuro-oncology

2014 Volume 118, Issue 1, Page(s) 49–60

Abstract: Vitamin D and its analogs have been shown to display anti-proliferative effects in a wide variety ... by its active metabolite, 1α, 25-dihydroxyvitamin D3 (calcitriol) acting mainly through vitamin D receptor (VDR) signaling ...

Abstract	Vitamin D and its analogs have been shown to display anti-proliferative effects in a wide variety of cancer types including glioblastoma multiforme (GBM). These anticancer effects are mediated by its active metabolite, 1α, 25-dihydroxyvitamin D3 (calcitriol) acting mainly through vitamin D receptor (VDR) signaling. In addition to its involvement in calcitriol action, VDR has also been demonstrated to be useful as a prognostic factor for some types of cancer. However, to our knowledge, there are no studies evaluating the expression of VDR protein and its association with outcome in gliomas. Therefore, we investigated VDR expression by using immunohistochemical analysis in human glioma tissue microarrays, and analyzed the association between VDR expression and clinico-pathological parameters. We further investigated the effects of genetic and pharmacologic modulation of VDR on survival and migration of glioma cell lines. Our data demonstrate that VDR is increased in tumor tissues when compared with VDR in non-malignant brains, and that VDR expression is associated with an improved outcome in patients with GBM. We also show that both genetic and pharmacologic modulation of VDR modulates GBM cellular migration and survival and that VDR is necessary for calcitriol-mediated effects on migration. Altogether these results provide some limited evidence supporting a role for VDR in glioma progression.
MeSH term(s)	Adult ; Age Factors ; Brain Neoplasms/metabolism ; Brain Neoplasms/mortality ; Brain Neoplasms/pathology ; Calcitriol/pharmacology ; Calcium Channel Agonists/pharmacology ; Cell Line, Tumor ; Cell Movement/genetics ; Cell Survival/drug effects ; Cell Survival/physiology ; Cyclin D1/metabolism ; Female ; Gene Expression Regulation, Neoplastic/drug effects ; Gene Expression Regulation, Neoplastic/genetics ; Glioblastoma/metabolism ; Glioblastoma/mortality ; Glioblastoma/pathology ; Humans ; Male ; Middle Aged ; Oncogene Proteins/metabolism ; RNA, Small Interfering/genetics ; RNA, Small Interfering/metabolism ; Receptors, Calcitriol/metabolism ; Sex Factors ; Time Factors ; Tissue Array Analysis
Chemical Substances	Calcium Channel Agonists ; Oncogene Proteins ; RNA, Small Interfering ; Receptors, Calcitriol ; Cyclin D1 (136601-57-5) ; Calcitriol (FXC9231JVH)
Language	English
Publishing date	2014-03-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	604875-4
ISSN	1573-7373 ; 0167-594X
ISSN (online)	1573-7373
ISSN	0167-594X
DOI	10.1007/s11060-014-1416-3
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Article ; Online: Effect of Daridorexant on the Pharmacokinetics of Midazolam, and on the Pharmacokinetics and Pharmacodynamics of Warfarin in Healthy Male Subjects.

Zenklusen, Isabelle / Dingemanse, Jasper / Reh, Christian / Gehin, Martine / Kaufmann, Priska

Drugs in R&D

2024 Volume 24, Issue 1, Page(s) 97–108

Abstract: Background and objectives: Daridorexant, a dual orexin receptor antagonist was recently approved for the treatment of insomnia at doses up to 50 mg once per night. This study investigated the effect of single-dose and multiple-dose daridorexant 50 mg at ...

Abstract	Background and objectives: Daridorexant, a dual orexin receptor antagonist was recently approved for the treatment of insomnia at doses up to 50 mg once per night. This study investigated the effect of single-dose and multiple-dose daridorexant 50 mg at steady state on the pharmacokinetics (PK) of the cytochrome P450 (CYP) 3A4-sensitive substrate midazolam, and the effect of single-dose daridorexant 50 mg on the PK and pharmacodynamics (PD) of the CYP2C9-sensitive substrate warfarin. Methods: In this prospective, single-center, open-label, fixed-sequence, phase I, drug-drug interaction study, 18 healthy male subjects sequentially received Treatment A, B, and C in three periods. Treatment A consisted of a single oral concomitant administration of midazolam 2 mg and warfarin 25 mg on day 1 of the first period. Treatment B consisted of one oral administration of daridorexant 50 mg followed 1 h later by a single oral dose of midazolam 2 mg concomitantly with a single oral dose of warfarin 25 mg on day 1 and a once-daily oral administration of daridorexant 50 mg for 6 days of the second period. Treatment C consisted of a single oral administration of daridorexant 50 mg at steady state followed 1 h later by a single oral administration of midazolam 2 mg on day 1 of the third period. Blood samples were assessed for midazolam and S-warfarin PK, and PD (international normalized ratio and factor VII). Noncompartmental PK parameters and PD variables were evaluated with geometric mean ratios and 90% confidence intervals of Treatment B/A versus C/A for midazolam, and treatment B/A for warfarin. Safety and tolerability of each treatment were also assessed. Results: Midazolam maximum plasma concentration (C Conclusions: Daridorexant at 50 mg is classified as a weak CYP3A4 inhibitor after single- and multiple-dose administration once daily at steady state. Daridorexant 50 mg did not induce CYP3A4 activity or inhibit CYP2C9 activity. Clinical trial registration: This trial (NCT05480488) was registered on 29 July, 2022.
MeSH term(s)	Humans ; Male ; Drug Interactions ; Midazolam/pharmacokinetics ; Midazolam/administration & dosage ; Adult ; Warfarin/pharmacokinetics ; Warfarin/administration & dosage ; Warfarin/pharmacology ; Young Adult ; Healthy Volunteers ; Triazoles/pharmacokinetics ; Triazoles/administration & dosage ; Triazoles/pharmacology ; Prospective Studies ; Orexin Receptor Antagonists/pharmacokinetics ; Orexin Receptor Antagonists/pharmacology ; Orexin Receptor Antagonists/administration & dosage ; Area Under Curve ; Imidazoles ; Pyrrolidines
Chemical Substances	Midazolam (R60L0SM5BC) ; Warfarin (5Q7ZVV76EI) ; daridorexant ; Triazoles ; Orexin Receptor Antagonists ; Imidazoles ; Pyrrolidines
Language	English
Publishing date	2024-03-13
Publishing country	New Zealand
Document type	Journal Article ; Clinical Trial, Phase I
ZDB-ID	2020476-0
ISSN	1179-6901 ; 1174-5886
ISSN (online)	1179-6901
ISSN	1174-5886
DOI	10.1007/s40268-024-00456-8
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Article ; Online: Differential affinity purification and mass spectrometry analysis of two nuclear pore complex isoforms in yeast S. cerevisiae.

Bensidoun, Pierre / Zenklusen, Daniel / Oeffinger, Marlene

STAR protocols

2023 Volume 4, Issue 3, Page(s) 102359

Abstract: Two isoforms of the nuclear pore complex (NPC) have been identified in the yeast S. cerevisiae, which coexist at the periphery of the nucleus and differ by the presence or absence of a nuclear basket. Here, we present a protocol to isolate the two types ... ...

Abstract	Two isoforms of the nuclear pore complex (NPC) have been identified in the yeast S. cerevisiae, which coexist at the periphery of the nucleus and differ by the presence or absence of a nuclear basket. Here, we present a protocol to isolate the two types of NPCs from the same cell extract and dissect their interactomes. We describe steps for powder preparation and magnetic bead conjunction and detail differential affinity purification and outcome evaluation through SDS-PAGE, silver staining, and mass spectrometry analysis. For complete details on the use and execution of this protocol, please refer to Bensidoun et al.
MeSH term(s)	Saccharomyces cerevisiae/metabolism ; Nuclear Pore/metabolism ; Saccharomyces cerevisiae Proteins/metabolism ; Protein Isoforms/metabolism ; Mass Spectrometry
Chemical Substances	Saccharomyces cerevisiae Proteins ; Protein Isoforms
Language	English
Publishing date	2023-06-15
Publishing country	United States
Document type	Journal Article
ISSN	2666-1667
ISSN (online)	2666-1667
DOI	10.1016/j.xpro.2023.102359
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Article ; Online: Probing the Conformational State of mRNPs Using smFISH and SIM.

Adivarahan, Srivathsan / Zenklusen, Daniel

Methods in molecular biology (Clifton, N.J.)

2020 Volume 2209, Page(s) 267–286

Abstract: mRNAs and lncRNAs assemble with RNA-binding proteins (RBPs) to form ribonucleoprotein complexes (RNPs ). The assembly of RNPs initiates co-transcriptionally, and their composition and organization is thought to change during the different steps of an RNP ...

Abstract	mRNAs and lncRNAs assemble with RNA-binding proteins (RBPs) to form ribonucleoprotein complexes (RNPs ). The assembly of RNPs initiates co-transcriptionally, and their composition and organization is thought to change during the different steps of an RNP life cycle. Modulation of RNP structural organization has been implicated in the regulation of different aspects of RNA metabolism, including establishing interactions between the 5' and 3' ends in regulating mRNA translation and turnover. In this chapter, we describe a single-molecule microscopy approach that combines fluorescent RNA in situ hybridization (smFISH) and structured illumination microscopy (SIM ) and allows to measure different aspects of RNP organization in cells, including distances between different regions within individual mRNAs, as well as the overall compaction state of RNAs in different subcellular compartments and environmental conditions. Moreover, we describe a detailed workflow required for image registration and analysis that allows determining distances at sub-diffraction resolution.
MeSH term(s)	In Situ Hybridization, Fluorescence/methods ; Nucleic Acid Conformation ; RNA, Long Noncoding/chemistry ; RNA, Messenger/chemistry ; RNA-Binding Proteins/chemistry ; Ribonucleoproteins/chemistry ; Single Molecule Imaging/methods
Chemical Substances	RNA, Long Noncoding ; RNA, Messenger ; RNA-Binding Proteins ; Ribonucleoproteins ; messenger ribonucleoprotein
Language	English
Publishing date	2020-11-17
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-0716-0935-4_17
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Book ; Online: Ghost Value Augmentation for $k$-ECSS and $k$-ECSM

Hershkowitz, D Ellis / Klein, Nathan / Zenklusen, Rico

2023

Abstract: We give a poly-time algorithm for the $k$-edge-connected spanning subgraph ($k$-ECSS) problem that returns a solution of cost no greater than the cheapest $(k+10)$-ECSS on the same graph. Our approach enhances the iterative relaxation framework with a ... ...

Abstract	We give a poly-time algorithm for the $k$-edge-connected spanning subgraph ($k$-ECSS) problem that returns a solution of cost no greater than the cheapest $(k+10)$-ECSS on the same graph. Our approach enhances the iterative relaxation framework with a new ingredient, which we call ghost values, that allows for high sparsity in intermediate problems. Our guarantees improve upon the best-known approximation factor of $2$ for $k$-ECSS whenever the optimal value of $(k+10)$-ECSS is close to that of $k$-ECSS. This is a property that holds for the closely related problem $k$-edge-connected spanning multi-subgraph ($k$-ECSM), which is identical to $k$-ECSS except edges can be selected multiple times at the same cost. As a consequence, we obtain a $\left(1+O\left(\frac{1}{k}\right)\right)$-approximation for $k$-ECSM, which resolves a conjecture of Pritchard and improves upon a recent $1+O\left(\frac{1}{k}\right)$ approximation of Karlin, Klein, Oveis Gharan, and Zhang. Moreover, we present a matching lower bound for $k$-ECSM, showing that our approximation ratio is tight up to the constant factor in $O\left(\frac{1}{k}\right)$, unless $P=NP$.
Keywords	Computer Science - Data Structures and Algorithms ; Mathematics - Combinatorics
Subject code	518
Publishing date	2023-11-16
Publishing country	us
Document type	Book ; Online
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Article ; Online: Nuclear mRNA metabolism drives selective basket assembly on a subset of nuclear pore complexes in budding yeast.

Bensidoun, Pierre / Reiter, Taylor / Montpetit, Ben / Zenklusen, Daniel / Oeffinger, Marlene

Molecular cell

2022 Volume 82, Issue 20, Page(s) 3856–3871.e6

Abstract: To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding ... ...

Abstract	To determine which transcripts should reach the cytoplasm for translation, eukaryotic cells have established mechanisms to regulate selective mRNA export through the nuclear pore complex (NPC). The nuclear basket, a substructure of the NPC protruding into the nucleoplasm, is thought to function as a stable platform where mRNA-protein complexes (mRNPs) are rearranged and undergo quality control prior to export, ensuring that only mature mRNAs reach the cytoplasm. Here, we use proteomic, genetic, live-cell, and single-molecule resolution microscopy approaches in budding yeast to demonstrate that basket formation is dependent on RNA polymerase II transcription and subsequent mRNP processing. We further show that while all NPCs can bind Mlp1, baskets assemble only on a subset of nucleoplasmic NPCs, and these basket-containing NPCs associate a distinct protein and RNA interactome. Taken together, our data point toward NPC heterogeneity and an RNA-dependent mechanism for functionalization of NPCs in budding yeast through nuclear basket assembly.
MeSH term(s)	Nuclear Pore/genetics ; Nuclear Pore/metabolism ; Saccharomycetales/genetics ; Saccharomycetales/metabolism ; RNA Polymerase II/genetics ; RNA Polymerase II/metabolism ; Proteomics ; Active Transport, Cell Nucleus/physiology ; Cell Nucleus/genetics ; Cell Nucleus/metabolism ; RNA, Messenger/genetics ; RNA, Messenger/metabolism ; Nuclear Pore Complex Proteins/genetics ; Nuclear Pore Complex Proteins/metabolism
Chemical Substances	RNA Polymerase II (EC 2.7.7.-) ; RNA, Messenger ; Nuclear Pore Complex Proteins
Language	English
Publishing date	2022-10-10
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Research Support, N.I.H., Extramural
ZDB-ID	1415236-8
ISSN	1097-4164 ; 1097-2765
ISSN (online)	1097-4164
ISSN	1097-2765
DOI	10.1016/j.molcel.2022.09.019
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Article: Lessons from (pre-)mRNA Imaging.

Adivarahan, Srivathsan / Zenklusen, Daniel

Advances in experimental medicine and biology

2019 Volume 1203, Page(s) 247–284

Abstract: Cells are complex assemblies of molecules organized into organelles and membraneless compartments, each playing important roles in ensuring cellular homeostasis. The different steps of the gene expression pathway take place within these various cellular ... ...

Abstract	Cells are complex assemblies of molecules organized into organelles and membraneless compartments, each playing important roles in ensuring cellular homeostasis. The different steps of the gene expression pathway take place within these various cellular compartments, and studying gene regulation and RNA metabolism requires incorporating the spatial as well as temporal separation and progression of these processes. Microscopy has been a valuable tool to study RNA metabolism, as it allows the study of biomolecules in the context of intact individual cells, embryos or tissues, preserving cellular context often lost in experimental approaches that require the collection and lysis of cells in large numbers to obtain sufficient material for different types of assays. Indeed, from the first detection of RNAs and ribosomes in cells to today's ability to study the behaviour of single RNA molecules in living cells, or the expression profile and localization of hundreds of mRNA simultaneously in cells, constant effort in developing tools for microscopy has extensively contributed to our understanding of gene regulation. In this chapter, we will describe the role various microscopy approaches have played in shaping our current understanding of mRNA metabolism and outline how continuous development of new approaches might help in finding answers to outstanding questions or help to look at old dogmas through a new lens.
MeSH term(s)	Animals ; Gene Expression ; Humans ; In Situ Hybridization, Fluorescence ; Molecular Imaging ; RNA Precursors ; RNA, Messenger/metabolism
Chemical Substances	RNA Precursors ; RNA, Messenger
Language	English
Publishing date	2019-12-06
Publishing country	United States
Document type	Journal Article ; Review
ISSN	2214-8019 ; 0065-2598
ISSN (online)	2214-8019
ISSN	0065-2598
DOI	10.1007/978-3-030-31434-7_9
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Article ; Online: Choosing the right exit: How functional plasticity of the nuclear pore drives selective and efficient mRNA export.

Bensidoun, Pierre / Zenklusen, Daniel / Oeffinger, Marlene

Wiley interdisciplinary reviews. RNA

2021 Volume 12, Issue 6, Page(s) e1660

Abstract: The nuclear pore complex (NPC) serves as a central gate for mRNAs to transit from the nucleus to the cytoplasm. The ability for mRNAs to get exported is linked to various upstream nuclear processes including co-transcriptional RNP assembly and processing, ...

Abstract	The nuclear pore complex (NPC) serves as a central gate for mRNAs to transit from the nucleus to the cytoplasm. The ability for mRNAs to get exported is linked to various upstream nuclear processes including co-transcriptional RNP assembly and processing, and only export competent mRNPs are thought to get access to the NPC. While the nuclear pore is generally viewed as a monolithic structure that serves as a mediator of transport driven by transport receptors, more recent evidence suggests that the NPC might be more heterogenous than previously believed, both in its composition or in the selective treatment of cargo that seek access to the pore, providing functional plasticity to mRNA export. In this review, we consider the interconnected processes of nuclear mRNA metabolism that contribute and mediate export competence. Furthermore, we examine different aspects of NPC heterogeneity, including the role of the nuclear basket and its associated complexes in regulating selective and/or efficient binding to and transport through the pore. This article is categorized under: RNA Export and Localization > Nuclear Export/Import RNA Turnover and Surveillance > Turnover/Surveillance Mechanisms RNA Interactions with Proteins and Other Molecules > Protein-RNA Interactions: Functional Implications.
MeSH term(s)	Active Transport, Cell Nucleus ; Cell Nucleus/metabolism ; Nuclear Pore/metabolism ; RNA Transport ; RNA, Messenger/genetics ; RNA, Messenger/metabolism
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2021-05-02
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ZDB-ID	2634714-3
ISSN	1757-7012 ; 1757-7004
ISSN (online)	1757-7012
ISSN	1757-7004
DOI	10.1002/wrna.1660
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Article ; Online: Measuring mRNA Decay in Budding Yeast Using Single Molecule FISH.

Trcek, Tatjana / Rahman, Samir / Zenklusen, Daniel

Methods in molecular biology (Clifton, N.J.)

2017 Volume 1720, Page(s) 35–54

Abstract: Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically engineered to inhibit transcription. However, ... ...

Abstract	Cellular mRNA levels are determined by the rates of mRNA synthesis and mRNA decay. Typically, mRNA degradation kinetics are measured on a population of cells that are either chemically treated or genetically engineered to inhibit transcription. However, these manipulations can affect the mRNA decay process itself by inhibiting regulatory mechanisms that govern mRNA degradation, especially if they occur on short time-scales. Recently, single molecule fluorescent in situ hybridization (smFISH) approaches have been implemented to quantify mRNA decay rates in single, unperturbed cells. Here, we provide a step-by-step protocol that allows quantification of mRNA decay in single Saccharomyces cerevisiae using smFISH. Our approach relies on fluorescent labeling of single cytoplasmic mRNAs and nascent mRNAs found at active sites of transcription, coupled with mathematical modeling to derive mRNA half-lives. Commercially available, single-stranded smFISH DNA oligonucleotides (smFISH probes) are used to fluorescently label mRNAs followed by the quantification of cellular and nascent mRNAs using freely available spot detection algorithms. Our method enables quantification of mRNA decay of any mRNA in single, unperturbed yeast cells and can be implemented to quantify mRNA turnover in a variety of cell types as well as tissues.
MeSH term(s)	Algorithms ; Cytoplasm/chemistry ; Cytoplasm/genetics ; In Situ Hybridization, Fluorescence/methods ; Kinetics ; Models, Biological ; RNA Stability ; RNA, Messenger/chemistry ; Saccharomyces cerevisiae/chemistry ; Saccharomyces cerevisiae/genetics ; Single-Cell Analysis/methods ; Transcription, Genetic
Chemical Substances	RNA, Messenger
Language	English
Publishing date	2017-11-29
Publishing country	United States
Document type	Journal Article
ISSN	1940-6029
ISSN (online)	1940-6029
DOI	10.1007/978-1-4939-7540-2_4
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