Papers by Annapaola Andolfo
Supplementary Figures and Tables
bioRxiv (Cold Spring Harbor Laboratory), Jun 22, 2024
Untargeted metabolomics by mass spectrometry technologies generates huge numbers of metabolite si... more Untargeted metabolomics by mass spectrometry technologies generates huge numbers of metabolite signals, requiring computational analyses for post-acquisition processing and databases for metabolite identification. Web-based data processing solutions frequently include only a part of the entire workflow thus requiring the use of different platforms. The R package "margheRita" enhances fragment matching accuracy and addresses the complete workflow for metabolomic profiling in untargeted studies based on liquid chromatography (LC) coupled with tandem mass spectrometry (MS/MS), especially in the case of data-independent acquisition, where all MS/MS spectra are acquired with high quantitative accuracy.
European journal of biochemistry, Apr 1, 2000
Human α1‐microglobulin (α1‐m; also called protein HC), a glycoprotein belonging to the lipocalin ... more Human α1‐microglobulin (α1‐m; also called protein HC), a glycoprotein belonging to the lipocalin superfamily, was isolated by sequential anion‐exchange chromatography and gel filtration from the urine of hemodialized patients and from amniotic fluid collected in the week 16–18 of pregnancy. The carbohydrate chains of the protein purified from the two sources, which are organized in two Asn‐linked and one Thr‐linked oligosaccharides, were structurally characterized using matrix‐assisted laser desorption ionization and electrospray mass spectrometry. The glycans attached to Thr5 are differently truncated NeuHexHexNAc sequences, and O‐glycosylation in the amniotic fluid protein is only partial. Asn96 has both diantennary and triantennary structures attached in the case of urinary α1‐m and only diantennary glycans in the amniotic fluid protein. The main carbohydrate units attached to Asn17 are in both proteins monosialylated and disialylated diantennary glycans. The position of the oligosaccharide chains in a three‐dimensional model of the protein, produced using the automated Swiss‐Model service, is also discussed.
Nucleic Acids Research
Facioscapulohumeral muscular dystrophy (FSHD) is one of the most prevalent neuromuscular disorder... more Facioscapulohumeral muscular dystrophy (FSHD) is one of the most prevalent neuromuscular disorders. The disease is linked to copy number reduction and/or epigenetic alterations of the D4Z4 macrosatellite on chromosome 4q35 and associated with aberrant gain of expression of the transcription factor DUX4, which triggers a pro-apoptotic transcriptional program leading to muscle wasting. As today, no cure or therapeutic option is available to FSHD patients. Given its centrality in FSHD, blocking DUX4 expression with small molecule drugs is an attractive option. We previously showed that the long non protein-coding RNA DBE-T is required for aberrant DUX4 expression in FSHD. Using affinity purification followed by proteomics, here we identified the chromatin remodeling protein WDR5 as a novel DBE-T interactor and a key player required for the biological activity of the lncRNA. We found that WDR5 is required for the expression of DUX4 and its targets in primary FSHD muscle cells. Moreover,...
Molecules
Physiologically, smooth muscle cells (SMC) and nitric oxide (NO) produced by endothelial cells st... more Physiologically, smooth muscle cells (SMC) and nitric oxide (NO) produced by endothelial cells strictly cooperate to maintain vasal homeostasis. In atherosclerosis, where this equilibrium is altered, molecules providing exogenous NO and able to inhibit SMC proliferation may represent valuable antiatherosclerotic agents. Searching for dual antiproliferative and NO-donor molecules, we found that furoxans significantly decreased SMC proliferation in vitro, albeit with different potencies. We therefore assessed whether this property is dependent on their thiol-induced ring opening. Indeed, while furazans (analogues unable to release NO) are not effective, furoxans’ inhibitory potency parallels with the electron-attractor capacity of the group in 3 of the ring, making this effect tunable. To demonstrate whether their specific block on G1-S phase could be NO-dependent, we supplemented SMCs with furoxans and inhibitors of GMP- and/or of the polyamine pathway, which regulate NO-induced SMC ...
Additional file 3: Supplementary Figure 3. (A) Quantification of the expression of COX2 (mAb #122... more Additional file 3: Supplementary Figure 3. (A) Quantification of the expression of COX2 (mAb #12282, Cell Signaling Technology, Danvers, MA, USA) in TNFα-stimulated and ASC-CM or -EV treated CH at day 3 and 6 analyzed by Western Blot. Data (n = 3 independent experiments) were normalized on GAPDH and expressed as relative values (CTRL = 1).(B) Representative Western Blot membrane for COX2 and GAPDH.
Additional file 1: Supplementary Figure 1. Representative images of EV incorporation by CH. EV de... more Additional file 1: Supplementary Figure 1. Representative images of EV incorporation by CH. EV derived from ASCGFP+ are indicated by green arrows, β-Tubulin was revealed with an Alexa Fluor® 568 conjugated antibody (red) and nuclei were stained with DAPI (blue). The scale bars indicate 10 μm and the orthogonal views referred to the EV encircled in yellow were obtained by Fiji software.
Antioxidants & Redox Signaling, 2021
Aims: Biliary diseases represent around 10% of all chronic liver diseases and affect both adults ... more Aims: Biliary diseases represent around 10% of all chronic liver diseases and affect both adults and children. Currently available biochemical tests detect cholestasis but not early liver fibrosis. Circulating extracellular vesicles (EVs) provide a noninvasive, real-time molecular snapshot of the injured organ. We thus aimed at searching for a panel of EV-based biomarkers for cholestasis-induced early liver fibrosis using mouse models. Results: Progressive and detectable histological evidence of collagen deposition and liver fibrosis was observed from day 8 after bile duct ligation (BDL) in mice. Whole transcriptome and small RNA sequencing analyses of circulating EVs revealed differentially enriched RNA species after BDL versus sham controls. Unsupervised hierarchical clustering identified a signature that allowed for discrimination between BDL and controls. In particular, 151 microRNAs (miRNAs) enriched in BDL-derived EVs were identified, of which 66 were conserved in humans. The liver was an important source of circulating EVs in BDL animals as evidenced by the enrichment of several hepatic mRNAs, such as Albumin and Haptoglobin. Interestingly, among experimentally validated miRNAs, miR192-5p, miR194-5p, miR22-3p, and miR29a-3p showed similar enrichment patterns also in EVs derived from 3,5-diethoxycarboncyl-1,4-dihydrocollidine-treated (drug-induced severe cholestasis) but not in mice with mild phenotype or non-cholestatic liver fibrosis.
uPAR-induced cell adhesion and migration: vitronectin provides the key
Nature Medicine
Innovative pro-regenerative treatment strategies for progressive multiple sclerosis (PMS), combin... more Innovative pro-regenerative treatment strategies for progressive multiple sclerosis (PMS), combining neuroprotection and immunomodulation, represent an unmet need. Neural precursor cells (NPCs) transplanted in animal models of multiple sclerosis have shown preclinical efficacy by promoting neuroprotection and remyelination by releasing molecules sustaining trophic support and neural plasticity. Here we present the results of STEMS, a prospective, therapeutic exploratory, non-randomized, open-label, single-dose-finding phase 1 clinical trial (NCT03269071, EudraCT 2016-002020-86), performed at San Raffaele Hospital in Milan, Italy, evaluating the feasibility, safety and tolerability of intrathecally transplanted human fetal NPCs (hfNPCs) in 12 patients with PMS (with evidence of disease progression, Expanded Disability Status Scale ≥6.5, age 18–55 years, disease duration 2–20 years, without any alternative approved therapy). The safety primary outcome was reached, with no severe adver...
Experimental …, 2007
... Authors: Tjwa, Marc × Sidenius, N Moons, Lieve Theunissen, Koen Moura, R Jansen,Sandra Andolf... more ... Authors: Tjwa, Marc × Sidenius, N Moons, Lieve Theunissen, Koen Moura, R Jansen,Sandra Andolfo, A De Mol, M Blasi, F Dewerchin, Mieke Verfaillie, Catherine Carmeliet, Peter. Issue Date: Sep-2007. Publisher: Elsevier Science Inc. ...
Biomedicines
Hypertrophic cardiomyopathy (HCM) is the most common genetic cardiomyopathy. The molecular mechan... more Hypertrophic cardiomyopathy (HCM) is the most common genetic cardiomyopathy. The molecular mechanisms determining HCM phenotypes are incompletely understood. Myocardial biopsies were obtained from a group of patients with obstructive HCM (n = 23) selected for surgical myectomy and from 9 unused donor hearts (controls). A subset of tissue-abundant myectomy samples from HCM (n = 10) and controls (n = 6) was submitted to laser-capture microdissection to isolate cardiomyocytes. We investigated the relationship among clinical phenotype, cardiac myosin proteins (MyHC6, MyHC7, and MyHC7b) measured by optimized label-free mass spectrometry, the relative genes (MYH7, MYH7B and MYLC2), and the MyomiR network (myosin-encoded microRNA (miRs) and long-noncoding RNAs (Mhrt)) measured using RNA sequencing and RT-qPCR. MyHC6 was lower in HCM vs. controls, whilst MyHC7, MyHC7b, and MyLC2 were comparable. MYH7, MYH7B, and MYLC2 were higher in HCM whilst MYH6, miR-208a, miR-208b, miR-499 were comparab...
NSCs induce downregulation of the activation cell surface marker CD44 on purified CD4+ T cells. C... more NSCs induce downregulation of the activation cell surface marker CD44 on purified CD4+ T cells. CD4+ T cells were purified by negative selection from total LNC, labelled with the vital dye CFSE, and cultured on CD3/CD28 coated mAb in the absence or the presence of NSCs, Th1 NSCs or Th2 NSCs for 72 h. Cells were surface stained with anti-CD4 and CD44 antibodies. Absolute fractions of CFSEdimCD44low CD4+ T cells are depicted. Data are expressed as mean % (±SD) from n ≥ 3 independent experiments. *p ≤ 0.05 and **p ≤ 0.01 vs. T cells.
Co-culturing with LNC and cytokine priming has no effects on NSC survival. LNC were labelled with... more Co-culturing with LNC and cytokine priming has no effects on NSC survival. LNC were labelled with the vital dye CFSE and co-cultured with NSC, Th1 NSCs or Th2 NSCs for 72 h as in Additional file 2: Fig. S2. Absolute fractions of CFSE− TO-PRO3+ CD4− cells, as an indicator of dead NSCs are expressed as mean % (±SD) from n ≥ 3 independent experiments.
Additional file 4: Supplementary Table 1. ASC features. Details of culture conditions (CTRL, Oste... more Additional file 4: Supplementary Table 1. ASC features. Details of culture conditions (CTRL, Osteoinduction and Adipoinduction) and performed assays are reported. Supplementary Table 2. Functional enriched processes identified with STRING through OA-related keywords (Chondro-, Metabol-,Catabol-, Inflamm- and Matrix). GO: Gene ontology identifier. Supplementary Table 3.Quantification of OA-related factors in ASC-CM (n = 3) expressed as mean ± SD. Details of the biological processes in which each factors is involved, according to Supplementary Table 2, are also provided. Supplementary Table 4. Principal Component Analysis (PCA) details by XLSTAT software. Number of factors analyzed for each OA-related keyword are reported in brackets. Supplementary Table 5. nLC-MS/MS quantification of OA-related factors in ASC-CM and ASC-EV (n = 3). Factors significantly different between CM and EV samples are in bold. Proteins more abundant in EV that in CM are highlighted in gray.
Scientific Reports, 2019
Corneal neo-vascularization (CNV) is a highly prevalent medical condition which impairs visual ac... more Corneal neo-vascularization (CNV) is a highly prevalent medical condition which impairs visual acuity. The role of specific proteins in modulating CNV has been extensively reported, although no studies have described the entire human proteome in CNV corneas. In this paper, we performed a proteomic analysis of vascularized vs healthy corneal stroma, in a CNV mouse model and in CNV-affected patients, with a specific focus on extracellular matrix (ECM) proteins. We identified and quantified 2315 murine proteins, 691 human proteins and validated 5 proteins which are differentially expressed in vascularized samples and conserved in mice and humans: tenascin-C and fibronectin-1 were upregulated, while decorin, lumican and collagen-VI were downregulated in CNV samples. Interestingly, among CNV patients, those affected with Acanthamoeba keratitis showed the highest levels of fibronectin-1 and tenascin-C, suggesting a specific role of these two proteins in Acanthamoeba driven corneal CNV. On...
Stem Cell Reports, 2019
Lymph nodes (LNs) are secondary lymphoid tissues that play a critical role in filtering the lymph... more Lymph nodes (LNs) are secondary lymphoid tissues that play a critical role in filtering the lymph and promoting adaptive immune responses. Surgical resection of LNs, radiation therapy, or infections may damage lymphatic vasculature and compromise immune functions. Here, we describe the generation of functional synthetic lympho-organoids (LOs) using LN stromal progenitors and decellularized extracellular matrix-based scaffolds, two basic constituents of secondary lymphoid tissues. We show that upon transplantation at the site of resected LNs, LOs become integrated into the endogenous lymphatic vasculature and efficiently restore lymphatic drainage and perfusion. Upon immunization, LOs support the activation of antigen-specific immune responses, thus acquiring properties of native lymphoid tissues. These findings provide a proof-of-concept strategy for the development of functional lympho-organoids suitable for restoring lymphatic and immune cell functions.
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Papers by Annapaola Andolfo