Virginie Magnone's research while affiliated with Université Côte d'Azur and other places

... Interestingly, the combination of SCENITH and scRNAseq analysis of renal carcinomas and juxta-tumoral tissues succeeded in the correlation of the metabolic profile and the metabolic gene expression. 250 Moreover, SCENITH can be employed in many other tumour settings and physiopathological conditions including for example the comprehension of cell death pathways that have important and multiple connections with metabolism and redox imbalance [254][255][256][257][258][259] (Fig. 5c). ...

... Several CSC biomarkers have been identified with useful applications to diagnosis, therapy, and prognosis. The paper by Morel et al. described the isolation of a subpopulation of the adrenocortical carcinoma (ACC) cell line H295R overexpressing the cell surface Hedgehog receptor Patched (Ptch1) [14]. Ptch1 is overexpressed in many cancer types and was shown to contribute to the resistance to chemotherapy in ACC. ...

... Trajectory analysis of monocyte subpopulations in BAT indicates that Ly6c high monocytes give rise to LAMs, which further bifurcate into terminally differentiated M2-like or matrix macrophages. 211 Dendritic cells Adipose tissue dendritic cells (ATDCs) have been previously associated with obesity, 212 and single-cell/nuclei analyses have now identified immuno-regulatory subpopulations of these cells in mouse and human WAT. 61,206 Two major subpopulations of conventional DCs (cDC1 and cDC2) are found across mouse eWAT and human sWAT. ...

... Indeed, aberrant expression of DNM3OS or associated miRNAs is common in many disorders especially those affecting the heart (el Azzouzi et al., 2013), lungs (C. Li et al., 2014), bones (Watanabe et al., 2008), kidneys (Denby et al., 2014;, and muscles (Arrighi et al., 2021;Hashemi Gheinani et al., 2015). For example, DNM3OS is thought to play a deleterious role in various bone diseases (Sun et al., 2018), fibrotic diseases (Nosalski et al., 2020), heart failure (el Azzouzi et al., 2013), chronic kidney diseases , or muscular dystrophies (Alexander et al., 2013). ...

... 43 NLUCAT1 is a large nuclear transcript and repressed genes within the antioxidant or cisplatinresponse networks, which represented a novel therapeutic target in LUAD. 44 Adenylate kinase 4 (AK4) was reported to modulate oxidative stress that enhanced lung cancer metastasis. 45 Besides, the aldehyde dehydrogenase 1A1 (ALDH1A1) confers erlotinib resistance by facilitating the ROS-RCS metabolic crosstalk, highlighting the robust associations between oxidative stress and drug resistance. ...

... And although this gene is very interesting, we could not obtain sufficient samples to analyze MBD4 as a subgroup. Next to the secondary driver mutations, differential expression of the genes FOXD1 [38], HES6 [39], ABHD6 [40], and PRC1 [41] is associated with metastasis formation in either BAP1 or SF3B1-mutated UMs. Unfortunately, we do not have transcriptomic information on most of the selected patients in this study. ...

... Interestingly, recent studies have shown excitatory/inhibitory imbalance in Fmr1 knockout mice 19 and report that the mice tend to have functionally impaired interneurons. 20 Perturbation in GABA signaling also occurs early in development in Fmr1 knockout mice; increased excitability was observed during critical period development and was thought to be due to a delay in the GABA functional switch that occurs during cortical development. 14,21,22 The GABA functional switch is characterized by a change in the effects of GABA in the developing brain, by which the neurotransmitter is initially excitatory, but then switches to being inhibitory due to a change in the type of K-Cl cotransporter expressed by developing neurons. ...

... iNKT cells can also be functionally classified into NKT1, NKT2, and NKT17 subsets based on the expression of transcriptional factors, T-bet, PLZF, GATA3, and RORγt (Constantinides and Bendelac, 2013;Lee et al., 2013). Recently, single-cell RNA sequencing (scRNA-seq) revealed comprehensive transcriptional profiles linked to the development, proliferation, maturation, and function of various iNKT cell subsets (Baranek et al., 2020;Engel et al., 2016). In addition, iNKT cells share overlapping developmental pathways, particularly with respect to cytokines, cell surface markers, and transcription factors needed for differentiation, with other innate T cell populations, including MAIT cells and γδ T cells (Harsha Krovi et al., 2020;Lee et al., 2020). ...

... However, several high-throughput scRNA-seq methods have been developed to overcome these limitations. By using long-read sequencing to analyze barcoded cDNA products derived from high-throughput scRNA-seq platforms, full-length RNA sequences can be detected to analyze alternative splicing events [4][5][6][7]. Nevertheless, the cost of long-read sequencing and the inability to detect non-polyadenylated transcripts hinder their widespread application. ...

... Large-scale single cell multiomics of in vitro multi-culture models to track rare airway epithelial lineage differentiation Recent single cell transcriptome studies of human primary lung tissues allowed for the mapping of cellular composition and lineage hierarchy at the single cell level [1][2][3]57 . However, epithelial cell types such as tuft cells, ionocytes, and pulmonary neuroendocrine cells (PNECs) are rare and therefore not amenable for either deep molecular characterization or inferring lineage trajectories from in vivo lung atlases 58 . ...