Differentiation of Mesenchymal Stem Cells Derived from Pancreatic Islets and Bone Marrow into Islet-Like Cell Phenotype

BACKGROUND:Regarding regenerative medicine for diabetes, accessible sources of Mesenchymal Stem Cells (MSCs) for induction of insular beta cell differentiation may be as important as mastering the differentiation process itself. METHODOLOGY/PRINCIPAL FINDINGS:In the present work, stem cells from pancreatic islets (human islet-mesenchymal stem cells, HI-MSCs) and from human bone marrow (bone marrow mesenchymal stem cells, BM-MSCs) were cultured in custom-made serum-free medium, using suitable conditions in order to induce differentiation into Islet-like Cells (ILCs). HI-MSCs and BM-MSCs were positive for the MSC markers CD105, CD73, CD90, CD29. Following this induction, HI-MSC and BM-MSC formed evident islet-like structures in the culture flasks. To investigate functional modifications after induction to ILCs, ultrastructural analysis and immunofluorescence were performed. PDX1 (pancreatic duodenal homeobox gene-1), insulin, C peptide and Glut-2 were detected in HI-ILCs whereas BM-ILCs only expressed Glut-2 and insulin. Insulin was also detected in the culture medium following glucose stimulation, confirming an initial differentiation that resulted in glucose-sensitive endocrine secretion. In order to identify proteins that were modified following differentiation from basal MSC (HI-MSCs and BM-MSCs) to their HI-ILCs and BM-ILCs counterparts, proteomic analysis was performed. Three new proteins (APOA1, ATL2 and SODM) were present in both ILC types, while other detected proteins were verified to be unique to the single individual differentiated cells lines. Hierarchical analysis underscored the limited similarities between HI-MSCs and BM-MSCs after induction of differentiation, and the persistence of relevant differences related to cells of different origin. CONCLUSIONS/SIGNIFICANCE:Proteomic analysis highlighted differences in the MSCs according to site of origin, reflecting spontaneous differentiation and commitment. A more detailed understanding of protein assets may provide insights required to master the differentiation process of HI-MSCs to functional beta cells based only upon culture conditioning. These findings may open new strategies for the clinical use of BM-MSCs in diabetes

A peptide-level multiple imputation strategy accounting for the different natures of missing values in proteomics data

Motivation: Quantitative mass spectrometry-based proteomics data are characterized by high rates of missing values, which may be of two kinds: missing completely-at-random (MCAR) and missing not-at-random (MNAR). Despite numerous imputation methods available in the literature, none account for this duality, for it would require to diagnose the missingness mechanism behind each missing value. Results: A multiple imputation strategy is proposed by combining MCAR-devoted and MNAR-devoted imputation algorithms. First, we propose an estimator for the proportion of MCAR values and show it is asymptotically unbiased under assumptions adapted to label-free proteomics data. This allows us to estimate the number of MCAR values in each sample and to take into account the nature of missing values through an original multiple imputation method. We evaluate this approach on simulated data and shows it outperforms traditionally used imputation algorithms. Availability The proposed methods are implemented in the R package imp4p (available on the CRAN Giai Gianetto (2020)), which is itself accessible through Prostar software. Contact [email protected] ; [email protected]

Pre- and Post-analytical Factors in Biomarker Discovery

The translation of promising biomarkers, which were identified in biomarker discovery experiments, to clinical assays is one of the key challenges in present-day proteomics research. Many so-called "biomarker candidates" fail to progress beyond the discovery phase, and much emphasis is placed on pre- and post-analytical variability in an attempt to provide explanations for this bottleneck in the biomarker development pipeline. With respect to such variability, there is a large number of pre- and post-analytical factors which may impact the outcomes of proteomics experiments and thus necessitate tight control. This chapter highlights some of these factors and provides guidance for addressing them on the basis of examples from previously published proteomics studies

Proteomics unveil a central role for peroxisomes in butyrate assimilation of the heterotrophic Chlorophyte alga Polytomella sp

Volatile fatty acids found in effluents of the dark fermentation of biowastes can be used for mixotrophic growth of microalgae, improving productivity and reducing the cost of the feedstock. Microalgae can use the acetate in the effluents very well, but butyrate is poorly assimilated and can inhibit growth above 1 gC.L -1 . The non-photosynthetic chlorophyte alga Polytomella sp. SAG 198.80 was found to be able to assimilate butyrate fast. To decipher the metabolic pathways implicated in butyrate assimilation, quantitative proteomics study was developed comparing Polytomella sp. cells grown on acetate and butyrate at 1 gC.L -1 . After statistical analysis, a total of 1772 proteins were retained, of which 119 proteins were found to be overaccumulated on butyrate vs. only 46 on acetate, indicating that butyrate assimilation necessitates additional metabolic steps. The data show that butyrate assimilation occurs in the peroxisome via the β-oxidation pathway to produce acetyl-CoA and further tri/dicarboxylic acids in the glyoxylate cycle. Concomitantly, reactive oxygen species defense enzymes as well as the branched amino acid degradation pathway were strongly induced.Although no clear dedicated butyrate transport mechanism could be inferred, several membrane transporters induced on butyrate are identified as potential condidates. Metabolic responses correspond globally to the increased needs for central cofactors NAD, ATP and CoA, especially in the peroxisome and the cytosol

SIN3 acts in distinct complexes to regulate the germline transcriptional program in C. elegans

Abstract The SIN3 transcriptional coregulator influences gene expression through multiple interactions that include histone deacetylases (HDACs). Haploinsufficiency and mutations in SIN3 are the underlying cause of Witteveen-Kolk syndrome and related intellectual disability (ID)/autism syndromes, emphasizing its key role in development. However, little is known about the diversity of its interactions and functions in developmental processes. Here we show that loss of SIN-3, the single SIN3 homologue in Caenorhabditis elegans , results in maternal effect sterility associated with deregulation of the germline transcriptome, including desilencing of X-linked genes. We identify at least two distinct SIN3 complexes containing specific HDACs, and show that they differentially contribute to fertility. Single cell smFISH reveals that in sin-3 mutants, the X chromosome becomes re-expressed prematurely and in a stochastic manner in individual germ cells. Furthermore, we identify histone residues whose acetylation increases in the absence of SIN3. Together, this work provides a powerful framework for the in vivo study of SIN3 and associated proteins

Constrained G4 structures unveil topology specificity of known and new G4 binding proteins

International audienceAbstract G-quadruplexes (G4) are non-canonical secondary structures consisting in stacked tetrads of hydrogen-bonded guanines bases. An essential feature of G4 is their intrinsic polymorphic nature, which is characterized by the equilibrium between several conformations (also called topologies) and the presence of different types of loops with variable lengths. In cells, G4 functions rely on protein or enzymatic factors that recognize and promote or resolve these structures. In order to characterize new G4-dependent mechanisms, extensive researches aimed at identifying new G4 binding proteins. Using G-rich single-stranded oligonucleotides that adopt non-controlled G4 conformations, a large number of G4-binding proteins have been identified in vitro, but their specificity towards G4 topology remained unknown. Constrained G4 structures are biomolecular objects based on the use of a rigid cyclic peptide scaffold as a template for directing the intramolecular assembly of the anchored oligonucleotides into a single and stabilized G4 topology. Here, using various constrained RNA or DNA G4 as baits in human cell extracts, we establish the topology preference of several well-known G4-interacting factors. Moreover, we identify new G4-interacting proteins such as the NELF complex involved in the RNA-Pol II pausing mechanism, and we show that it impacts the clastogenic effect of the G4-ligand pyridostatin

Size-dependent ecotoxicity of barium titanate particles: the case of Chlorella vulgaris green algae.

Studies have been demonstrating that smaller particles can lead to unexpected and diverse ecotoxicological effects when compared to those caused by the bulk material. In this study, the chemical composition, size and shape, state of dispersion, and surface's charge, area and physicochemistry of micro (BT MP) and nano barium titanate (BT NP) were determined. Green algae Chlorella vulgaris grown in Bold's Basal (BB) medium or Seine River water (SRW) was used as biological indicator to assess their aquatic toxicology. Responses such as growth inhibition, cell viability, superoxide dismutase (SOD) activity, adenosine-5-triphosphate (ATP) content and photosynthetic activity were evaluated. Tetragonal BT (~170 nm, 3.24 m(2) g(-1) surface area) and cubic BT (~60 nm, 16.60 m(2) g(-1)) particles were negative, poorly dispersed, and readily aggregated. BT has a statistically significant effect on C. vulgaris growth since the lower concentration tested (1 ppm), what seems to be mediated by induced oxidative stress caused by the particles (increased SOD activity and decreased photosynthetic efficiency and intracellular ATP content). The toxic effects were more pronounced when the algae was grown in SRW. Size does not seem to be an issue influencing the toxicity in BT particles toxicity since micro- and nano-particles produced significant effects on algae growth.201

Regulation of Postsynaptic Function by the Dementia-Related ESCRT-III Subunit CHMP2B

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Thirty-thousand-year-old distant relative of giant icosahedral DNA viruses with a pandoravirus morphology

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Nut directs p300-dependent, genome-wide H4 hyperacetylation in male germ cells

Nuclear protein in testis (Nut) is a universal oncogenic driver in the highly aggressive NUT midline carcinoma, whose physiological function in male germ cells has been unclear. Here we show that expression of Nut is normally restricted to post-meiotic spermatogenic cells, where its presence triggers p300-dependent genome-wide histone H4 hyperacetylation, which is essential for the completion of histone-to-protamine exchange. Accordingly, the inactivation of Nut induces male sterility with spermatogenesis arrest at the histone-removal stage. Nut uses p300 and/or CBP to enhance acetylation of H4 at both K5 and K8, providing binding sites for the first bromodomain of Brdt, the testis-specific member of the BET family, which subsequently mediates genome-wide histone removal. Altogether, our data reveal the detailed molecular basis of the global histone hyperacetylation wave, which occurs before the final compaction of the male genome. A transcription-independent histone hyperacetylation is associated with near-total histone replacement during mouse spermatogenesis. Shiota et al. show the oncogenic factor Nut is expressed in post-meiotic male germ cells, where it recruits p300 and/or CBP and enhances histone H4K5 and H4K8 acetylation, leading to histone-to-protamine replacement