Francesco Marabita

Francesco Marabita
Karolinska Institutet | KI · Department of Oncology-Pathology - SciLifeLab

PhD

About

65
Publications
7,208
Reads
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3,134
Citations
Introduction
In my current research position, I target the resolution of biological questions through integrative bioinformatics, with a focus on epigenomics. I have been involved in developing and testing different analysis pipelines but also in evaluating biological questions through comprehensive data analysis.
Additional affiliations
January 2018 - present
SciLifeLab - Karolinska Institutet
Position
  • Bioinformatician
January 2016 - present
Karolinska Institutet
Position
  • Professor (Assistant)
January 2012 - December 2015
Karolinska Institutet
Position
  • PostDoc Position
Education
January 2008 - December 2011
Università degli Studi di Milano-Bicocca
Field of study
  • Translational and Molecular Medicine
October 2004 - March 2007
University of Bologna
Field of study
  • Pharmaceutical Biotechnology
October 2001 - October 2004
University of Bologna
Field of study
  • Biotechnology

Publications

Publications (65)
Article
Full-text available
The high-throughput analysis of microRNAs (miRNAs) circulating within the blood of healthy and diseased individuals is an active area of biomarker research. Whereas quantitative real-time reverse transcription polymerase chain reaction (qPCR)-based methods are widely used, it is yet unresolved how the data should be normalized. Here, we show that a...
Article
Full-text available
ABSTRACT Regular endurance exercise training induces beneficial functional and health effects in human skeletal muscle. The putative contribution to the training response of the epigenome as a mediator between genes and environment has not been clarified. Here we investigated the contribution of DNA methylation and associated transcriptomic changes...
Article
Full-text available
The proper identification of differentially methylated CpGs is central in most epigenetic studies. The Illumina HumanMethylation450 BeadChip is widely used to quantify DNA methylation; nevertheless, the design of an appropriate analysis pipeline faces severe challenges due to the convolution of biological and technical variability and the presence...
Article
Full-text available
Unlabelled: Polymorphisms in the interleukin-28B (IL28B) region are associated with spontaneous and treatment-induced viral clearance in hepatitis C virus (HCV) infection. Nevertheless, it is unknown whether genetic variation at the IL28B locus influences the natural history of chronic HCV infection. Thus, we asked whether an association between I...
Article
MicroRNAs are small noncoding RNAs that regulate gene expression post-transcriptionally. Here we applied microRNA profiling to 17 human lymphocyte subsets to identify microRNA signatures that were distinct among various subsets and different from those of mouse lymphocytes. One of the signature microRNAs of naive CD4+ T cells, miR-125b, regulated t...
Article
We explored opportunities for personalized and predictive health care by collecting serial clinical measurements, health surveys, genomics, proteomics, autoantibodies, metabolomics, and gut microbiome data from 96 individuals who participated in a data-driven health coaching program over a 16-month period with continuous digital monitoring of activ...
Preprint
Full-text available
In order to explore opportunities for personalized and predictive health care, we collected serial clinical measurements, health surveys and multiomics profiles (genomics, proteomics, autoantibodies, metabolomics and gut microbiome) from 96 individuals. The participants underwent data-driven health coaching over a 16-month period with continuous di...
Conference Paper
Acute myeloid leukemia (AML) is the most common leukemia in adults and the prognosis is dismal. The heterogeneity of driver mutations in AML from one patient to another is significant. Although new treatment targets and modalities have recently been introduced, a lack of therapies to cover the entire spectrum of molecularly distinct AML classes rem...
Article
Full-text available
Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and...
Article
Full-text available
Aim: Accumulating evidence links epigenetic age to diseases and age-related conditions, but little is known about its association with multiple sclerosis (MS). Materials & methods: We estimated epigenetic age acceleration measures using DNA methylation from blood or sorted cells of MS patients and controls. Results: In blood, sex (p = 4.39E-05) and...
Article
Full-text available
We introduce and develop a method that demonstrates that the algorithmic information content of a system can be used as a steering handle in the dynamical phase space, thus affording an avenue for controlling and reprogramming systems. The method consists of applying a series of controlled interventions to a networked system while estimating how th...
Preprint
Full-text available
Multi-omics approaches use a diversity of high-throughput technologies to profile the different molecular layers of living cells. Ideally, the integration of this information should result in comprehensive systems models of cellular physiology and regulation. However, most multi-omics projects still include a limited number of molecular assays and...
Article
Full-text available
The human leukocyte antigen (HLA) haplotype DRB1*15:01 is the major risk factor for multiple sclerosis (MS). Here, we find that DRB1*15:01 is hypomethylated and predominantly expressed in monocytes among carriers of DRB1*15:01. A differentially methylated region (DMR) encompassing HLA-DRB1 exon 2 is particularly affected and displays methylation-se...
Article
Full-text available
Background: Regulatory T cells (Tregs) expressing the transcription factor FOXP3 are crucial mediators of self-tolerance, preventing autoimmune diseases but possibly hampering tumor rejection. Clinical manipulation of Tregs is of great interest, and first-in-man trials of Treg transfer have achieved promising outcomes. Yet, the mechanisms governin...
Preprint
Full-text available
We introduce a new conceptual framework and a model-based interventional calculus to steer, manipulate, and reconstruct the dynamics and generating mechanisms of non-linear dynamical systems from partial and disordered observations based on the contributions of each of the systems, by exploiting first principles from the theory of computability and...
Article
Full-text available
Background Chronic obstructive pulmonary disease (COPD) patients often show skeletal muscle dysfunction that has a prominent negative impact on prognosis. The study aims to further explore underlying mechanisms of skeletal muscle dysfunction as a characteristic systemic effect of COPD, potentially modifiable with preventive interventions (i.e. musc...
Article
Full-text available
Cigarette smoking is an established environmental risk factor for Multiple Sclerosis (MS), a chronic inflammatory and neurodegenerative disease, although a mechanistic basis remains largely unknown. We aimed at investigating how smoking affects blood DNA methylation in MS patients, by assaying genome-wide DNA methylation and comparing smokers, form...
Article
Full-text available
We introduce a conceptual framework and an interventional calculus to reconstruct the dynamics of, steer, and manipulate systems based on their intrinsic algorithmic probability using the universal principles of the theory of computability and algorithmic information. By applying sequences of controlled interventions to systems and networks, we est...
Article
Full-text available
Regulatory T cells (Tregs) control key events of immune tolerance, primarily by suppression of effector T cells. We previously revealed that Tregs rapidly suppress T cell receptor (TCR)-induced calcium store depletion in conventional CD4+CD25− T cells (Tcons) independently of IP3 levels, consequently inhibiting NFAT signaling and effector cytokine...
Article
Systems medicine and systems biology have inherent educational challenges. These have largely been addressed either by providing new masters programs or by redesigning undergraduate programs. In contrast, short courses can respond to a different need: they can provide condensed updates for professionals across academia, the clinic, and industry. Th...
Article
Multiple Sclerosis (MS) is a chronic inflammatory and demyelinating disease of the central nervous system. MS likely results from a complex interplay between predisposing causal gene variants (the strongest influence coming from HLA class II locus) and environmental risk factors such as smoking, infectious mononucleosis and lack of sun exposure/vit...
Article
Full-text available
Arsenic, a carcinogen with immunotoxic effects, is a common contaminant of drinking water and certain food worldwide. We hypothesized that chronic arsenic exposure alters gene expression, potentially by altering DNA methylation of genes encoding central components of the immune system. We therefore analyzed the transcriptomes (by RNA sequencing) an...
Article
Full-text available
Azacitidine (Aza) is first-line treatment for patients with high-risk myelodysplastic syndromes (MDS), although its precise mechanism of action is unknown. We performed the first study to globally evaluate the epigenetic effects of Aza on MDS bone marrow progenitor cells assessing gene expression (RNA seq), DNA methylation (Illumina 450k) and the h...
Article
Full-text available
Objective: Members of the transient receptor potential (TRP) channels are involved in mediating the electrical excitability and stimulus-secretion coupling in the pancreatic β-cells. The expression and the relative abundance of different TRP channels in the human β-cells are unknown. The objective of this study was to examine the expression of the...
Article
Full-text available
Background and aim: The diagnosis of primary sclerosing cholangitis (PSC) is difficult due to the lack of sensitive and specific biomarkers, as is the early diagnosis of cholangiocarcinoma (CC), a complication of PSC. The aim of this study was to identify specific serum miRNAs as diagnostic biomarkers for PSC and CC. Methods: The levels of 667 m...
Chapter
The epigenome is th ecollection of all epigenetic modifications occurring on a genome. To properly generate, analyze, and understand epigenomic data has become increasingly important in basic and applied research, because epigenomic modifications have been broadly associated with differentiation, development, and disease processes, thereby also con...
Article
Full-text available
Chronic Obstructive Pulmonary Disease (COPD) patients are characterized by heterogeneous clinical manifestations and patterns of disease progression. Two major factors that can be used to identify COPD subtypes are muscle dysfunction/wasting and co-morbidity patterns. We hypothesized that COPD heterogeneity is in part the result of complex interact...
Article
Full-text available
Background and Aims The PNPLA3 I148M sequence variant favors hepatic lipid accumulation and confers susceptibility to hepatic fibrosis and hepatocellular carcinoma. The aim of this study was to estimate the effect size of homozygosity for the PNPLA3 I148M variant (148M/M) on the fibrosis progression rate (FPR) and the interaction with age at infect...
Article
Following the success of genome-wide association studies, it is now important to unravel interactions between genes as well as between genes and environment. Here we discuss how to interpret higher order statistical interactions in terms of underlying biological processes purportedly generating such dependencies. In this chapter, we specifically re...
Article
Full-text available
Activated lymphocytes release nano-sized vesicles (exosomes) containing microRNAs that can be monitored in the bloodstream. We asked whether elicitation of immune responses is followed by release of lymphocyte-specific microRNAs. We found that, upon activation in vitro, human and mouse lymphocytes down-modulate intracellular miR-150 and accumulate...
Article
Full-text available
The altered expression of miRNA has been associated with Crohn's disease (CD) and ulcerative colitis (UC). AIM: To establish specific miRNA expression patterns in the serum and mucosa of IBD patients (UC and CD with colonic involvement) at different stages of the disease. METHODS: Serum and biopsies from 9 active CD (aCD), 9 inactive CD (iCD), 9 ac...
Article
The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstream analyses...
Article
Full-text available
Motivation: The Illumina Infinium 450 k DNA Methylation Beadchip is a prime candidate technology for Epigenome-Wide Association Studies (EWAS). However, a difficulty associated with these beadarrays is that probes come in two different designs, characterized by widely different DNA methylation distributions and dynamic range, which may bias downstr...
Article
Full-text available
Autoimmune Hepatitis (AIH) is an unresolving inflammation of the liver of unknown cause. Diagnosis requires the exclusion of other conditions and the presence of characteristic features such as specific autoantibodies. Presently, these autoantibodies have relatively low sensitivity and specificity and are identified by immunostaining of cells or ti...

Projects

Project (1)