Imperial College London

DrEnricoPetretto

Faculty of MedicineInstitute of Clinical Sciences

Senior Lecturer
 
 
 
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Contact

 

+44 (0)20 3313 1468enrico.petretto Website

 
 
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Location

 

231ICTEM buildingHammersmith Campus

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Summary

 

Publications

Publication Type
Year
to

110 results found

Cuartero S, Weiss FD, Dharmalingam G, Guo Y, Ing-Simmons E, Masella S, Robles-Rebollo I, Xiao X, Wang Y-F, Barozzi I, Djeghloul D, Amano MT, Niskanen H, Petretto E, Dowell RD, Tachibana K, Kaikkonen MU, Nasmyth KA, Lenhard B, Natoli G, Fisher AG, Merkenschlager Met al., 2018, Control of inducible gene expression links cohesin to hematopoietic progenitor self-renewal and differentiation, NATURE IMMUNOLOGY, Vol: 19, Pages: 932-+, ISSN: 1529-2908

JOURNAL ARTICLE

Min ATL, Langley SR, Tan CF, Fang CJ, Khoo CM, Leow MK-S, Khoo EYH, Moreno Moral A, Pravenec M, Rotival M, Sadananthan SA, Velan SS, Venkataraman K, Chong YS, Lee YS, Xueling S, Stunkel W, Liu MH, Tai ES, Petretto Eet al., 2018, Ethnicity-specific skeletal muscle transcriptional signatures and their relevance to insulin resistance in Singapore., J Clin Endocrinol Metab

Context: Insulin resistance (IR) and obesity differ between ethnic groups in Singapore, with the Malays being more obese yet less IR than Asian-Indians. However, the molecular basis underlying these differences are not clear. Objective: As the skeletal muscle (SM) is metabolically relevant to IR, we investigated molecular pathways in SM that are associated with ethnic differences in IR, obesity and related traits. Design, Setting and Main Outcome measures: We integrated transcriptomic, genomic and phenotypic analyses in 156 healthy subjects representing three major ethnicities in the Singapore Adult Metabolism Study. Patients: This study contains Chinese (n=63), Malay (n=51) and Asian-Indian (n=42) males, aged 21-40 years, without systemic diseases. Results: We found remarkable diversity in the SM transcriptome between the three ethnicities with >8,000 differentially expressed genes (40% of all genes expressed in SM). Comparison with blood transcriptome from a separate Singaporean cohort showed that >95% of SM expression differences between ethnicities were unique to SM. We identified a network of 46 genes that were specifically down-regulated in Malays, suggesting dysregulation of components of cellular respiration in SM of Malay individuals. We also report 28 differentially expressed gene-clusters, four of which were also enriched for genes that were found in GWAS of metabolic traits and disease and correlated with variation in IR, obesity and related traits. Conclusion: We identified extensive gene expression changes in SM between the three Singaporean ethnicities, and report specific genes and molecular pathways that might underpin and explain the differences in IR between these ethnic groups.

JOURNAL ARTICLE

Moreno-Moral A, Bagnati M, Koturan S, Ko J-H, Fonseca C, Harmston N, Game L, Martin J, Ong V, Abraham DJ, Denton CP, Behmoaras J, Petretto Eet al., 2018, Changes in macrophage transcriptome associate with systemic sclerosis and mediate GSDMA contribution to disease risk, ANNALS OF THE RHEUMATIC DISEASES, Vol: 77, Pages: 596-601, ISSN: 0003-4967

JOURNAL ARTICLE

Olona A, Terra X, Ko J-H, Grau-Bove C, Pinent M, Ardevol A, Diaz AG, Moreno-Moral A, Edin M, Bishop-Bailey D, Zeldin DC, Aitman TJ, Petretto E, Blay M, Behmoaras Jet al., 2018, Epoxygenase inactivation exacerbates diet and aging-associated metabolic dysfunction resulting from impaired adipogenesis, MOLECULAR METABOLISM, Vol: 11, Pages: 18-32, ISSN: 2212-8778

JOURNAL ARTICLE

Pereira M, Petretto E, Gordon S, Bassett JHD, Williams GR, Behmoaras Jet al., 2018, Common signalling pathways in macrophage and osteoclast multinucleation, JOURNAL OF CELL SCIENCE, Vol: 131, ISSN: 0021-9533

JOURNAL ARTICLE

Rodriguez-Martinez A, Posma JM, Ayala R, Neves AL, Anwar M, Petretto E, Emanueli C, Gauguier D, Nicholson JK, Dumas M-Eet al., 2018, MWASTools: an R/bioconductor package for metabolome-wide association studies, BIOINFORMATICS, Vol: 34, Pages: 890-892, ISSN: 1367-4803

JOURNAL ARTICLE

Sigmundsson K, Ojala JRM, Öhman MK, Österholm A-M, Moreno-Moral A, Domogatskaya A, Chong LY, Sun Y, Chai X, Steele JAM, George B, Patarroyo M, Nilsson A-S, Rodin S, Ghosh S, Stevens MM, Petretto E, Tryggvason Ket al., 2018, Culturing functional pancreatic islets on α5-laminins and curative transplantation to diabetic mice., Matrix Biol, Vol: 70, Pages: 5-19

The efficacy of islet transplantation for diabetes treatment suffers from lack of cadaver-derived islets, islet necrosis and long transfer times prior to transplantation. Here, we developed a method for culturing mouse and human islets in vitro on α5-laminins, which are natural components of islet basement membranes. Adhering islets spread to form layers of 1-3 cells in thickness and remained normoxic and functional for at least 7 days in culture. In contrast, spherical islets kept in suspension developed hypoxia and central necrosis within 16 h. Transplantation of 110-150 mouse islets cultured on α5-laminin-coated polydimethylsiloxane membranes for 3-7 days normalized blood glucose already within 3 days in mice with streptozotocin-induced diabetes. RNA-sequencing of isolated and cultured mouse islets provided further evidence for the adhesion and spreading achieved with α5-laminin. Our results suggest that use of such in vitro expanded islets may significantly enhance the efficacy of islet transplantation treatment for diabetes.

JOURNAL ARTICLE

Solimena M, Schulte AM, Marselli L, Ehehalt F, Richter D, Kleeberg M, Mziaut H, Knoch K-P, Parnis J, Bugliani M, Siddiq A, Joerns A, Burdet F, Liechti R, Suleiman M, Margerie D, Syed F, Distler M, Gruetzmann R, Petretto E, Moreno-Moral A, Wegbrod C, Soenmez A, Pfriem K, Friedrich A, Meinel J, Wollheim CB, Baretton GB, Scharfmann R, Nogoceke E, Bonifacio E, Sturm D, Meyer-Puttlitz B, Boggi U, Saeger H-D, Filipponi F, Lesche M, Meda P, Dahl A, Wigger L, Xenarios I, Falchi M, Thorens B, Weitz J, Bokvist K, Lenzen S, Rutter GA, Froguel P, von Buelow M, Ibberson M, Marchetti Pet al., 2018, Systems biology of the IMIDIA biobank from organ donors and pancreatectomised patients defines a novel transcriptomic signature of islets from individuals with type 2 diabetes, DIABETOLOGIA, Vol: 61, Pages: 641-657, ISSN: 0012-186X

JOURNAL ARTICLE

Srivastava PK, van Eyll J, Godard P, Mazzuferi M, Delahaye-Duriez A, Van Steenwinckel J, Gressens P, Danis B, Vandenplas C, Foerch P, Leclercq K, Mairet-Coello G, Cardenas A, Vanclef F, Laaniste L, Niespodziany I, Keaney J, Gasser J, Gillet G, Shkura K, Chong S-A, Behmoaras J, Kadiu I, Petretto E, Kaminski RM, Johnson MRet al., 2018, A systems-level framework for drug discovery identifies Csf1R as an anti-epileptic drug target, NATURE COMMUNICATIONS, Vol: 9, ISSN: 2041-1723

JOURNAL ARTICLE

Aday S, Halevy I, Anwar M, Besnier M, Beltrami C, Herman A, Sahoo S, Petretto E, Angelini GD, Peer D, Emanueli Cet al., 2017, Artificial exosomes for post-ischemic vascular regeneration, Congress of the European-Society-of-Cardiology (ESC), Publisher: OXFORD UNIV PRESS, Pages: 33-33, ISSN: 0195-668X

CONFERENCE PAPER

Anwar M, Saif J, Aday S, Biglino G, Heesom K, Angelini G, Petretto E, Emanueli Cet al., 2017, A Bioinformatics Approach Reveals Mechanism of Pericardial Fluid Exosome Action in Promoting Ischemia in Diabetic Patients, Scientific Sessions of the American-Heart-Association / Resuscitation Science Symposium, Publisher: LIPPINCOTT WILLIAMS & WILKINS, ISSN: 0009-7322

CONFERENCE PAPER

Baliga NS, Bjoerkegren JLM, Boeke JD, Boutros M, Crawford NPS, Dudley AM, Farber CR, Jones A, Levey AI, Lusis AJ, Mak HC, Nadeau JH, Noyes MB, Petretto E, Seyfried NT, Steinmetz LM, Vonesch SCet al., 2017, The State of Systems Genetics in 2017 commentary, CELL SYSTEMS, Vol: 4, Pages: 7-15, ISSN: 2405-4712

JOURNAL ARTICLE

Beltrami C, Besnier M, Shantikumar S, Shearn AIU, Rajakaruna C, Laftah A, Sessa F, Spinetti G, Petretto E, Angelini GD, Emanueli Cet al., 2017, Human Pericardial Fluid Contains Exosomes Enriched with Cardiovascular-Expressed MicroRNAs and Promotes Therapeutic Angiogenesis, MOLECULAR THERAPY, Vol: 25, Pages: 679-693, ISSN: 1525-0016

JOURNAL ARTICLE

Chen T-D, Rotival M, Chiu L-Y, Bagnati M, Ko J-H, Srivastava PK, Petretto E, Pusey CD, Lai P-C, Aitman TJ, Cook HT, Behmoaras Jet al., 2017, Identification of Ceruloplasmin as a Gene that Affects Susceptibility to Glomerulonephritis Through Macrophage Function, GENETICS, Vol: 206, Pages: 1139-1151, ISSN: 0016-6731

JOURNAL ARTICLE

Coan PM, Hummel O, Diaz AG, Barrier M, Alfazema N, Norsworthy PJ, Pravenec M, Petretto E, Huebner N, Aitman TJet al., 2017, Genetic, physiological and comparative genomic studies of hypertension and insulin resistance in the spontaneously hypertensive rat, DISEASE MODELS & MECHANISMS, Vol: 10, Pages: 297-306, ISSN: 1754-8403

JOURNAL ARTICLE

Heinig M, Adriaens ME, Schafer S, van Deutekom HWM, Lodder EM, Ware JS, Schneider V, Felkin LE, Creemers EE, Meder B, Katus HA, Ruehle F, Stoll M, Cambien F, Villard E, Charron P, Varro A, Bishopric NH, George AL, dos Remedios C, Moreno-Moral A, Pesce F, Bauerfeind A, Rueschendorf F, Rintisch C, Petretto E, Barton PJ, Cook SA, Pinto YM, Bezzina CR, Hubner Net al., 2017, Natural genetic variation of the cardiac transcriptome in non-diseased donors and patients with dilated cardiomyopathy, GENOME BIOLOGY, Vol: 18, ISSN: 1474-760X

JOURNAL ARTICLE

Imprialou M, Petretto E, Bottolo L, 2017, Expression QTLs Mapping and Analysis: A Bayesian Perspective., Pages: 189-215

The aim of expression Quantitative Trait Locus (eQTL) mapping is the identification of DNA sequence variants that explain variation in gene expression. Given the recent yield of trait-associated genetic variants identified by large-scale genome-wide association analyses (GWAS), eQTL mapping has become a useful tool to understand the functional context where these variants operate and eventually narrow down functional gene targets for disease. Despite its extensive application to complex (polygenic) traits and disease, the majority of eQTL studies still rely on univariate data modeling strategies, i.e., testing for association of all transcript-marker pairs. However these "one at-a-time" strategies are (1) unable to control the number of false-positives when an intricate Linkage Disequilibrium structure is present and (2) are often underpowered to detect the full spectrum of trans-acting regulatory effects. Here we present our viewpoint on the most recent advances on eQTL mapping approaches, with a focus on Bayesian methodology. We review the advantages of the Bayesian approach over frequentist methods and provide an empirical example of polygenic eQTL mapping to illustrate the different properties of frequentist and Bayesian methods. Finally, we discuss how multivariate eQTL mapping approaches have distinctive features with respect to detection of polygenic effects, accuracy, and interpretability of the results.

BOOK CHAPTER

Krishnan ML, Van Steenwinckel J, Schang A-L, Yan J, Arnadottir J, Le Charpentier T, Csaba Z, Dournaud P, Cipriani S, Auvynet C, Titomanlio L, Pansiot J, Ball G, Boardman JP, Walley AJ, Saxena A, Mirza G, Fleiss B, Edwards AD, Petretto E, Gressens Pet al., 2017, Integrative genomics of microglia implicates DLG4 (PSD95) in the white matter development of preterm infants, NATURE COMMUNICATIONS, Vol: 8, ISSN: 2041-1723

JOURNAL ARTICLE

McDermott-Roe C, Leleu M, Rowe GC, Palygin O, Bukowy JD, Kuo J, Rech M, Hermans-Beijnsberger S, Schaefer S, Adami E, Creemers EE, Heinig M, Schroen B, Arany Z, Petretto E, Geurts AMet al., 2017, Transcriptome-wide co-expression analysis identifies LRRC2 as a novel mediator of mitochondrial and cardiac function, PLOS ONE, Vol: 12, ISSN: 1932-6203

JOURNAL ARTICLE

Moreno-Moral A, Pesce F, Behmoaras J, Petretto Eet al., 2017, Systems Genetics as a Tool to Identify Master Genetic Regulators in Complex Disease., Pages: 337-362

Systems genetics stems from systems biology and similarly employs integrative modeling approaches to describe the perturbations and phenotypic effects observed in a complex system. However, in the case of systems genetics the main source of perturbation is naturally occurring genetic variation, which can be analyzed at the systems-level to explain the observed variation in phenotypic traits. In contrast with conventional single-variant association approaches, the success of systems genetics has been in the identification of gene networks and molecular pathways that underlie complex disease. In addition, systems genetics has proven useful in the discovery of master trans-acting genetic regulators of functional networks and pathways, which in many cases revealed unexpected gene targets for disease. Here we detail the central components of a fully integrated systems genetics approach to complex disease, starting from assessment of genetic and gene expression variation, linking DNA sequence variation to mRNA (expression QTL mapping), gene regulatory network analysis and mapping the genetic control of regulatory networks. By summarizing a few illustrative (and successful) examples, we highlight how different data-modeling strategies can be effectively integrated in a systems genetics study.

BOOK CHAPTER

Nefzger CM, Rossello FJ, Chen J, Liu X, Knaupp AS, Firas J, Paynter JM, Pflueger J, Buckberry S, Lim SM, Williams B, Alaei S, Faye-Chauhan K, Petretto E, Nilsson SK, Lister R, Ramialison M, Powell DR, Rackham OJL, Polo JMet al., 2017, Cell Type of Origin Dictates the Route to Pluripotency, CELL REPORTS, Vol: 21, Pages: 2649-2660, ISSN: 2211-1247

JOURNAL ARTICLE

Petretto E, 2017, Genetics of Neurodevelopmental Disorders: Connecting The Dots in The Brain, 18th International Congress of Developmental Biology, Publisher: ELSEVIER SCIENCE BV, Pages: S4-S4, ISSN: 0925-4773

CONFERENCE PAPER

Rackham OJL, Langley SR, Oates T, Vradi E, Harmston N, Srivastava PK, Behmoaras J, Dellaportas P, Bottolo L, Petretto Eet al., 2017, A Bayesian Approach for Analysis of Whole-Genome Bisulfite Sequencing Data Identifies Disease-Associated Changes in DNA Methylation, GENETICS, Vol: 205, Pages: 1443-1458, ISSN: 0016-6731

JOURNAL ARTICLE

Schafer S, Viswanathan S, Widjaja AA, Lim W-W, Moreno-Moral A, DeLaughter DM, Ng B, Patone G, Chow K, Khin E, Tan J, Chothani SP, Ye L, Rackham OJL, Ko NSJ, Sahib NE, Pua CJ, Zhen NTG, Xie C, Wang M, Maatz H, Lim S, Saar K, Blachut S, Petretto E, Schmidt S, Putoczki T, Guimaraes-Camboa N, Wakimoto H, van Heesch S, Sigmundsson K, Lim SL, Soon JL, Chao VTT, Chua YL, Tan TE, Evans SM, Loh YJ, Jamal MH, Ong KK, Chua KC, Ong B-H, Chakaramakkil MJ, Seidman JG, Seidman CE, Hubner N, Sin KYK, Cook SAet al., 2017, IL-11 is a crucial determinant of cardiovascular fibrosis, NATURE, Vol: 552, Pages: 110-+, ISSN: 0028-0836

JOURNAL ARTICLE

Srivastava PK, Bagnati M, Delahaye-Duriez A, Ko J-H, Rotival M, Langley SR, Shkura K, Mazzuferi M, Danis B, van Eyll J, Foerch P, Behmoaras J, Kaminski RM, Petretto E, Johnson MRet al., 2017, Genome-wide analysis of differential RNA editing in epilepsy, GENOME RESEARCH, Vol: 27, Pages: 440-450, ISSN: 1088-9051

JOURNAL ARTICLE

Srivastava PK, Roncon P, Lukasiuk K, Gorter JA, Aronica E, Pitkanen A, Petretto E, Johnson MR, Simonato Met al., 2017, Meta-Analysis of MicroRNAs Dysregulated in the Hippocampal Dentate Gyrus of Animal Models of Epilepsy, ENEURO, Vol: 4, ISSN: 2373-2822

JOURNAL ARTICLE

Suresh J, Harmston N, Lim KK, Kaur P, Jin HJ, Lusk JB, Petretto E, Tolwinski NSet al., 2017, An embryonic system to assess direct and indirect Wnt transcriptional targets, SCIENTIFIC REPORTS, Vol: 7, ISSN: 2045-2322

JOURNAL ARTICLE

Delahaye-Duriez A, Srivastava P, Shkura K, Langley SR, Laaniste L, Moreno-Moral A, Danis B, Mazzuferi M, Foerch P, Gazina EV, Richards K, Petrou S, Kaminski RM, Petretto E, Johnson MRet al., 2016, Rare and common epilepsies converge on a shared gene regulatory network providing opportunities for novel antiepileptic drug discovery, GENOME BIOLOGY, Vol: 17, ISSN: 1474-760X

JOURNAL ARTICLE

Diaz-Montana JJ, Rackham OJL, Diaz-Diaz N, Petretto Eet al., 2016, Web-based Gene Pathogenicity Analysis (WGPA): a web platform to interpret gene pathogenicity from personal genome data, BIOINFORMATICS, Vol: 32, Pages: 635-637, ISSN: 1367-4803

JOURNAL ARTICLE

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